I don't think they should have Ultron in the first Avengers movie. I just don't see any way of introducing him right off the bat. The Avengers wouldn't like a very competent team if right after they come together, one of their own creates a villain that can destroy humanity.
I have a radical idea that I know for sure they'll never use: Count Nefaria. No I'm not kidding, just hear me out for a minute, cuz this guy's no slouch.
Luchino Nefaria is this big wealthy aristocrat who's got a big fat company, not unlike Stark. Nefaria's is a private military company with a buttload of defense contracts (there's more of them to go around once Stark Industries stopped making weapons...). He's also secretly consorting with HYDRA, and secretly populating his private army with super-powered bad guys (in violation of the Super-Human Test Ban Treaty). If you've been watching the latest season of 24 (or seen State of Play), you can guess where this is going.
So I'd make taking down Hulk into the Avengers' first big action scene as a team. Meanwhile, there's this slow boil behind the scenes of Nefaria's and his company building power with HYDRA. There'd be plenty of Lethal Legion henchmen (and a few returning baddies from the previous movies), to give our heroes grief throughout. It could all build to an action-packed finale with all the Avengers + SHIELD vs. the Lethal Legion + HYDRA. And (straight out of the comics), Nefaria betrays his own guys when he absorbs and supercharges all their powers into himself, and fights all the Avengers alone.
There's a lot of blanks to fill in there, but I could definitely see it. And for god's sake, I hope the go ahead and just make it 2 1/2 hours.