For me, I'd have to say Khyber the Huntsman. While I liked Omniverse overall, I have to admit that the biggest reason I watched was for Khyber. Why I liked him:
-I'd say his introduction was reminiscent of Vilgax in the Original Series. In the shadows watching, intimidating, mysterious, and charismatic. You have no idea who this guy is but you know he's a serious threat.
-His motives. Khyber is different from other villains who fought Ben for the Omnitrix. Where most of them wanted the Omnitrix for power, or to sell it to the former for profit, Khyber sought out the Omnitrix to be his greatest trophy, to prove that he was"the greatest hunter in the galaxy". It's funny, I've never found myself too interested in the hunter villains, but I guess in the universe of Ben 10, I liked it as it offered something different in a villain for that series.
-The Nemetrix. Even though it was Psychobos who created the Nemetrix, you know that this device was fit to be Khyber's signature weapon. I really liked the idea of the Nemetrix, transforming it's wearer into vicious predatory alien animals that were actually the natural predators of the aliens in the Omnitrix. It was creative for what you could call the anti-thesis to the Omnitrix. Plus, it added a new bunch of alien transformations to like outside the Omnitrix (favorite predator is Tyrannopede). I wish we could've seen more of the Nemetrix and more predators for the Omnitrix aliens.
And there's other stuff like his appearance, personality (he's calm, intimidating, patient), etc.
And there you go. Khyber is my favorite villain in the Ben 10 franchise. I really hope he returns in the Ben 10 Reboot (if it turns out good)