Pros and Cons of each show in the original continuity
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I think that every series in the franchise had their good points as well as things that they could've done better, so I'll try and present my opinion on all of these. This will be a very long post so bear with me.
Original Series
Pros: For me it was the best show when it came to character development and growth, and the three protagonists in Ben, Gwen and Grandpa Max were great. Ben and Gwen are imperfect and that's what makes them relatable, it makes you root for them, and they balance each other so well as characters (I know that a lot of the fandom hate their bickering but I think that it's pretty much how siblings would act). Max is a great mentor figure even before his reveal as a Plumber, and after that it is fascinating to learn about his past and the Men In Black-esque organisation which were the Plumbers. The universe felt so diverse with magic, mutants, aliens, bounty hunters at the same time as remaining grounded, and Ben's rogues gallery were all unique, even the one off villains like Clancy, and the writers got really creative with the range of plots while not making it too outlandish (except for that cursed Christmas episode) The aliens were at their most unique, balanced and interesting here as well and it felt so exciting to see Ben use them, and the Omnitrix looked cool. This is a personal preference but I think that the art style was the best in the original and just added to the experience. I just have a lot of praise for the original and there are so many other things which just add to why this series is my favourite out of all of them.Cons: Ben suffered a character regression during season 3, and while I think that developing a bit of an ego is natural for a kid after kicking butt as a hero, they pushed it way too far sometimes even for a 10 year old's standards. The episode based structure of the show also started to become less viable towards the end of the OS which is why the final season felt a little underwhelming sometimes because there was basically no build up towards the Negative 10 two parter (though Secret of the Omnitrix was fantastic.). Also, the Forever Knights really could've been done better, and while Enoch was alright, Driscoll sucked even with his apparent past ties with Max and his high up status as the Forever King. It also wasn't explained how Vilgax got frozen after being defeated by Ben for the first time, or how he escaped the Null Void by SOTO, and there are occasionally instances where the classic series doesn't fully explain events, but I think that this is mainly tied to the episode based format.
Alien Force Seasons 1-2
Pros: It was 100% the right move to go towards a story driven structure after the original series and Alien Force did that well. I think that the setup that the series promised was excellent too: the Highbreed were unique villains and the whole secret invasion thing that they had going on was really intriguing. The DNAliens were really interesting as well given that they are in fact innocent humans under parasitic control and could've led to some compelling moral conundrums. Some of Ben's new aliens had pretty cool designs, and the fact that Grandpa Max wasn't beside them made the story more interesting. After the summer fun adventure of the original, the stakes were raised here in a story set up in the Tennysons own home town with an invasion of aliens who have bodysnatchers at their disposal who can use ID masks to blend in to society meaning that not many can be trusted. Tons of potential which was sometimes fulfilled (for example, "Alone Together" in my opinion was a masterpiece of an episode and really showed what the writers could do), but sometimes the execution did not match the quality of the ideas. Also Paradox was awesome and to this day is still my favourite character - partially inspired by the Doctor from Doctor Who but maintaining his unique personality and backstory.Cons: It felt too try-hardy especially in the first season. Basically every episode was set at night which made the series look dreary, Max was apparently killed off in only the 6th episode, Ben became too serious and felt like a different character, they turned Gwen into a boring token female , and then there was Kevin who went through a transition which can best be described as the Joker suddenly becoming Han Solo. Rather than being the insane dark counterpart of Ben, Kevin is now the 'bad boy' who does illegal deals in the black market, has a body build befitting of someone 5 years older than him, with a cool car and an apparently dark past which he is trying to move past. His redemption should've never made sense but it would've been more believable if it were stretched out over the entire of S1, and it was cringe to see how they rushed the Gwevin ship even while completely ignoring the context of the original series. The alien designs were good tbf and I really liked some such as Big Chill and Swampfire. However in terms of powers they were pretty much fusions of the original aliens except more powerful, making the original aliens feel redundant and less special because the new aliens were stupidly overpowered. The retcons sucked - particularly the Plumbers retcon which turned them from an earth only organisation into an intergalactic police force (am I the only one who thinks that the AF storyline would've actually worked better with the Earth plumbers? ). And in the first two seasons there was no sign of Gwen using any magic and instead using Green Lantern-esque constructs, which was explained to being the descendant of a species of aliens called Anodites which explains her power. I think the episode involving the reveal even straight up said that magic did not exist in this universe which sucked. Ben shouting out the names of his aliens was cringey and was pretty obviously there for marketing purposes.
Alien Force Season 3 ( deserves a different section since it changes so much from the first 2 seasons)
Pros: This season was a bit more balanced when it came to setting, with a good number of episodes being set in the day to dispel the dark theme a bit. The plots were a lot more varied and we did see the return of some familiar faces and old aliens which was nice. The characters (especially Ben) are not so one dimensional anymore which can be good but that could work both ways…I’ll get to that. The main thing that I am incredibly grateful to Season 3 of Alien Force is how they unretconned their previous retcon of Gwen’s powers just enough to allow magic to exist again with the reintroduction of Charmcaster, with Gwen’s Anodite heritage explaining her innate ability at magic rather than being the sole basis for her powers which is a bit more acceptable although I am still not a fan of Anodites in general. Some of the episodes were admittedly good, my personal favourite being “Above and Beyond”. Also, despite looking like what happens when you fuse Tony the Tiger with Wolverine, Rath is easily one of the best parts of season 3 and UAF in general because of his personality.Cons: Plotholes. Lots and lots of plotholes along with some more retcons. Why is the Omnitrix suddenly a wireless receiver connecting to Primus when it was clearly established that it was a DNA storage device? Why can the Omnitrix now just slip off Ben’s hand like a regular watch despite the fact that it is bonded to him? How did Ben's aliens manage to escape the Omnitrix when they tried to hack it? Kevin is now also an alien rather than being a mutated human. This itself isn’t that bad but the reveal of Max’s old partner Devin Levin just begs the question: why did Max never reach out to 11 year old Kevin in the original series and try to help his ex-partner’s son? Then there's Ben's personality - he does a complete 180 from being a mature and serious individual to an arrogant and immature jerk who's full of himself. Now granted, I like how this Ben isn't Mr Perfect anymore and has flaws, but S3 Alien Force Ben makes 10 year old Ben feel like a mature hero in comparison - one of the reasons that I liked "The Con of Rath" is because Ben himself was only on screen for about three minutes lol. While some of the S3 stories were good, some were just awful such as "Fool's Gold". And AF Vilgax was generic and boring without any of the menace that he had in the original series.
Ultimate Alien
Pros: By this point you've basically got used to the trio and I think that they felt so much more like real people rather than cliches like they did in Alien Force. They blended Ben's heroic nature with his cockiness and fun-loving nature pretty decently most of the time, Gwen was far better since she was now feisty again like she was in the original while also being the level headed and smartest, and Kevin was as snarky as ever. Their interactions and chemistry with each other is pretty much the main thing which drives Ultimate Alien and differentiates it from Alien Force. I liked the themes that they were going for such as Ben dealing with fame and the consequences of that, and personally I actually found the one-off episodes such as "Video Games" pretty enjoyable with the problems only arising when they came right in the middle of a story arc. The Andromeda 5 were interesting aliens and each of their episodes is unique in its own right, Aggregor was a solid villain and the Andromeda 5/Map of Infinity arc was probably the peak of Ultimate Alien and its storytelling. I also appreciate how they attempted to give Charmcaster her own arc.Cons: Oh boy...I have a few. It once again felt like it was trying too hard to be dark and gritty, with the main offender being the Ultimate Kevin arc. To this day I still have no clue why Ben was willing to spare Vilgax in AF, save the guardian of the Perplahexahedron at the cost of getting the last piece of the Map of Infinity, but then just suddenly decides that Kevin needs to die despite having more personal connection to him than any of the others? The Ultimate Kevin arc did have potential and I see the ideas which the writers were trying to go for - perhaps even suggesting Ben getting dangerously close to becoming the coldhearted Ben 10,000. But once again it is the ideas vs execution aspect which UA does not deliver on, and the fact that Kevin is never at all held responsible for his actions because "the powers made him do it" is frankly stupid - surely that should apply to other insane superpowered characters in fiction like the Green Goblin? There were numerous other plot holes which just kinda ruined the story a bit, and the Diagon arc was a massive snooze fest with the only interesting part being Old George (before he was revealed to actually be a good guy). The rest of the Diagon arc had the most generic villain, Vilgax being shoehorned into the plot and the lamest final battle, ending with the eternally memeable line: "You....stabbed me!" because that's all the fight consisted of. The Ultimate Aliens felt like something out of a fanfiction and asides from Ultimate Echo Echo they were a little underwhelming, not to mention how we only got about 8 Ultimate Aliens and they were scarcely used despite literally being in the show's title. The animation also got a bit clunky though I can't blame the animators much given that their budget wasn't that high.
Omniverse
Pros: I appreciate how the series tried to inject some fresh air and adventure back into the franchise. Most of the episodes were now set at day and the ones which were at night still looked good possibly because of the artstyle and colour pallete. The concept of Undertown was genius and it is a very nice transition phase from the present day to Ben 10,000s future where aliens and humans are living together pretty much in harmony. Some of the new rogues and villlains were great - Khyber was very unique and threatening in the earlier seasons of Omniverse and although some people don't like the Nemetrix, I thought that it suited Khyber's needs and gave Ben a new challenge. Malware was excellently implemented and the arc involving him was one of the best story arcs that the franchise has ever had, especially in terms of Ben himself growing as a character. There were some really interesting ideas in there such as the concept of Ben 23 who highlighted just how important Grandpa Max was to Ben's growth, especially when you compare 23 side by side with Prime Ben. They tried to add a lot of diversity back to the universe which again, I appreciate, at the same time as giving almost every alien from across the franchise some screen time. Rook was also a surprisingly good character and was someone whom you could root for.Cons: While UAF felt like it was trying too hard to be dark, Omniverse felt like it was trying too hard to be humourous. For example, Ben always shooting for Humoungasaur but getting a different alien. Granted this was sorta funny until when the Omnitrix gave him Humoungasaur for the first time in the season 1 finale (which was admittedly a sweet payoff) but after that it got VERY annoying. The most infamous example of this is the Contemalia scene in the final episode where Ben sees these beings as the closest thing to his heart. You'd expect that to be Grandpa Max, or his parents, or Gwen, or even Rook, right? Nope, they appear as godamn Mr Smoothy Mascots. This exaggerated focus on humour dampens a lot of moments in the series and makes it less impactful. Ben himself feels aloof as a character and doesn't seem to recognise the gravity of a situation most of the time. I like him being cocky and taunting villains but a lot of the time he feels more immature than his 10 year old self which is incredibly frustrating since he has been through so much and to see him regress like that feels wrong (though imo he isn't quite as bad as AF S3 Ben). It has it's fair share of plotholes and retcons as well, which are more commonly hated by the fandom than the UAF because the OV team were blatantly obvious about them. The most infamous of these is the Rooters arc and while I understand that they were trying to make it more like the original series with mutants and magic and whatnot, fixing retcons with more retcons is not right.
Overall every series has its strong points as well as areas where they could've improved upon, and although my favourite is the original I like how all of them brought something new to the table.
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@coreofthesun In regards to the DNAliens, it would've been nice if they actually did tackle some compelling moral conundrums with them. That was one of my biggest criticisms of the Highbreed arc. It didn't handle the element of DNAliens actually being innocent humans well. Even when the characters knew that the DNAliens were actually humans, they still willingly got many DNAliens killed and didn't really bat an eye on the fact that they were humans and should be saved instead until they were in the middle of the final battle at the end of season 2.
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@Tactical-Ochoa Exactly. The reveal in "Max Out" was mind blowing and it really is a shame that they didn't take that into consideration. The closest that we got was in "Inside Man" where Ben had to choose between saving the infected Tyler or stopping the DNAliens from carrying out their plan. I think that him reluctantly choosing the latter option would've been a pretty heavy character moment but he doesn't in the end.
What really annoyed me is that in the S2 Finale, Cooper managed to build DNA repair guns...and the main characters still killed tons of DNAliens. Ben himself flip-flopped between being unwilling to hurt them and killing them with no issues whatsoever in the heat of battle.
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My personal favourite will always be the classic series. It felt the most unique and diverse to me and whenever I watch it I feel my childlike wonder coming back. UAF and Omniverse were more polished shows but didn't feel the same to me. I do have a soft spot for Omniverse because I went through some difficult times when I was a teenager and watching Omniverse always cheered me up, whether that be through the expressive art style or the character interactions between Ben and Rook. Although sometimes the adventures could get ridiculous, I still enjoyed it and it was certainly a breath of fresh air as @coreofthesun mentioned.
I can understand why people liked the UAF era the best, but it didn't appeal to me because it kept constantly trying to remind you that "This is a serious show" and a lot of the hype seemed to be built up around the characters having matured. It felt like a "What if DC made Ben 10?" concept except they actually made it into a series. The retcons were a bit blatant, at least Omniverse attempted to explain their retcons rather than shoving them in your face without explaining. I really wasn't a fan of how they changed Gwen into a boring and almost soft character especially given that OS Gwen was an inspiration to me to be strong and independent as a girl. Although Ultimate Alien felt like Alien Force lite, Gwen was way better as a character there. Story driven structures are good and I appreciate the Highbreed arc a lot more looking back on it, but the execution of it could've been better with such an excellent premise. Dwayne McDuffie (may his good soul rest in peace) was a talented writer and I like a lot of his work, but he took the series in a direction which wasn't really that of a sequel.
All the shows have their good points but in my heart the original continuity ended with "Goodbye and Good Riddance", with the others taking place in alternate universes (I do believe this theory because there is no way to explain the retcons otherwise). I would've loved a sequel show to the original in the style of Generator Rex which I think does a superior job at telling a story with a more mature tone while still balancing it with humour.
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they all had their good and bad points so I don't really have a favorite series, they are not perfect by themselves.