I think I remember you talking about the DNA Aliens before but I'm not sure if my memory serves well. There has been lots of writers that hasn't really paid attention to the overall story of the season and what would happen before and later in the story arc. They most certainly didn't taken a look at the original series because if they have then I think Alien Force and onwards would been a very different show. None the less UAF still do hold a higher spot for me then the original series in my opinion.
Yeah on top of all the people Micheal knowingly murdered then got sent to the null void with the plumber re-awarding Kevin and Gwen their plumbers badge back. Except Ben didn't got his badge back meaning he was able to stop the rooters a year later as a result. So at least that paid off. However around 2 months later Gwen made Cooper free Darkstar/Micheal out of the null void to seek his aid on stopping the highbreed invasion in return he'd be free. He ratted out and Kevin , Gwen and Ben. Just let it drift aside after all the humans he MURDERED and they didn't took it seriously. Micheal would later be formally arrested again when rook stop micheal from evading custody at Friedkin University. This can't go unnoticed they let Darkstar continue his activities.
Also Remember in Ulimate Alien how Gwen wanted to save Kevin when he went insane after absorbing all that power from the omnitrix while begging Ben not to kill Kevin. Because Ben wanted to save many other lives that are under threat by "Ultimate Kevin". Irony here.