Um, you just answered it right there. They didn't clear up that villain arc, just gave him a cheesy out. The ballsy thing to do, and in my estimation the only thing to do, was to kill Sylar or have New York go up. Instead, they fluffed it, with the Heroes winning, but that gosh-darn bad guy gets to live!
IMO, trying to play a bit with the comic book type hokiness will kill them because the writers and creator have NO IDEA what to do with this series. Is it a drama? It tries very hard at times to be a serious drama, usually in vain. Is it a comedy? It tries very hard at times to be funny, and Hiro usually pulls it off. Is it a hokey comic book show? Absolutely not, which is why Sylar getting away at the end was sooo damned STUPID.
Until this show actually gains anything resembling focus, it will remain what it always has been--an okay show with some cool angles. Not great, but worth watching for now.
It IS a comic book show, but that doesn't make it hokey.
Whatever...that's part of the glory of the series to me. Killing off Sylar would have been dumb from a "This is a comic book show about superheroes and villians, with only one main villian."
It is absolutely SO that kind of show. And I love the hell out of it for that.
Who needs more mystery dramas??? Go watch Lost for that (which I watch as well and love for different reasons.)