And while it's pretty clear that Thanos will play some role in Marvel's "second phase" of filmmaking, it seems less likely that the Mad Titan will go from his role in the first film--using other powerful villains as pawns--to a hands-on battle against The Avengers without a support staff in place.
With that in mind, who might Whedon tap to help Thanos? We've got some ideas.
This would be an extremely hard sell, but it's got to be mentioned, since he was alongside Thanos for much of The Infinity Gauntlet, which is widely assumed to be at least part of the basis for any major Thanos-driven story in Avengers 2.
A powerful being with a great visual, he could work well, assuming Marvel could figure out a way to make his mythology work that's similar to what they did with Thor and the Asgardians--he's not THE devil, he's a guy whose likeness has inspired tales of the devil in some cultures, or something like that. Even then, he'd have to be a pretty well-represented visual, becuase you can't have him look too much like a typical Satan without losing the reality Marvel has built up through their previous films and/or running the risk of alienating parts of the mainstream audience.
Kang the Conqueror
Like Loki, it's hard to see him necessarily working with Thanos as much as working his own angle, with Thanos providing support staff, and the pair potentially coming into conflict with one another at some point. He's a great cosmic villain, though, and relies more on science than on magic, so he'd fit in better with Thanos than Mephisto or even Loki. He's also got a history with the Cosmic Cube, meaning that he's got a connection (even if its' tenuous) to the storyline of The Avengers.
He's also--and this is important for a role like playing second fiddle to a larger villain--a legitimate threat all his own who would be able to steal away while the good guys are fighting Thanos and live to be a threat unto himself in a future film, if all is done correctly.
Because he's a robot, there's a good chance that the average moviegoer won't buy him as a principal antagonist until they get a sense for what he's all about. Introducing him in the context of working for a familiar villain is one of the best ways to "sell" him to non-comics readers, and if need be they could show a modified version of his actual origin.
And, again, he's a great villain for a future film. On top of that? There'll be a major Ultron crossover coming up soon in the comics, so that gives Marvel Studios the possibility of doing an Ultron War adaptation at some point down the road if the character caught on with the fans.
The obvious choice, of course, is Alexis Denisof's Chitauri leader, so far just called "The Other." It's unclear exactly who he is, but we've got a few ideas for who it might be if you're interested.
The most likely choice is Chthon, an evil elder god (sometimes referred to as The Other in the comic book source material) who could match up with Thanos in terms of an overall mission statement. There's also the possibility of The Controller, a guy with connections to Thanos that go all the way back to his origin story.
Someone who's powerful enough to team up with Krona and take on an all-star team of Justice Leaguers and Avengers, there's really no reason he couldn't be used in a similar capacity to Thanos. Appearing at the last minute after Thanos has been defeated, it wouldn't much much sense (and would seem kind of formulaic) if Thanos were revealed to be working for him directly...but that doesn't preclude The Grandmaster from having planned on the outcome all along.
Bonus: Who can you count out?
It's unlikely we'll see Loki teaming with Thanos again, although I wouldn't put it past the God of Mischief to make an appearance to throw the battle in one direction or another. Who's even less likely? The Red Skull. While he's been teased as a possible future villain for The Avengers and he's someone who has a lot of history with the "tesseract"/Cosmic Cube, he'll likely have a giant, smoking hole in his chest compliments of Captain America: The Winter Soldier, and chances are good he'll be out of circulation for a while.