I think that the concept of arch-enemies' constantly coming back is realistic. There's a lot of rebel and terrorist groups all over the world who has been trying to topple the government/institution they're fighting against for decades, because they're fighting for something they think is right.Take a look at Iraq, they've been bombed for several decades but that hasn't kept the rebels from running away scared.
The Ultimate villains are doing the same thing, and none of them consider themselves to be evil, while the rest are just insane. Like some of you guys said, they believe that they're also fighting for an important cause, whether it is selfish or not, or if it some perverted or distorted ideology.
At least the people who are keeping hold of the captured super-villains are a lot smarter. They're not just stupidly throwing them in some stupid jail with some stupid guards that they can easily get out off. In the Ultimate Universe, SHIELD uses every means possible to make sure that the super-baddies stay put, but of course it is never perfect. I'm really interested in how they're going to bring back Doc Ock after Fury turned his tentacles to soup.
I'm really looking forward to Hobgoblin, regardless of who the hell he is. Bendis loves playing with our heads, so we can never really be sure if it would be Harry or not.