It seems like Thanos is the main villain of the entire Marvel universe. For those that read the comics, assuming Thanos is defeated in Avengers 3, how many other bigger/better stories are out there that can be used for phase 4 (for the current crop of charachters we've already seen)
The big ones I can think of are The Masters of Evil, who are basically the anti-Avengers. The roster has changed over the years but they could easily use some of the villains from previous movies that aren't dead. Red Skull would be a perfect leader for that if (when) he returns, and they can use Abomination as well. They can use Phase 4 to introduce villains that would form that team too, like Amorah the Enchantress.
The main one that I want as a follow-up to Thanos would be Kang the Conqueror. He'd make a great grey-area villain compared to Thanos' ultimate evil and Ultron's unwavering goal of extinction. He's trying to save the future from the actions of The Avengers which sets off a chain of events that destroys the world in his timeline, but does so by conquering Earth in the past.
A Kree-Skrull War storyline would be good too, which could be followed up by Secret Invasion.
Or Dormammu, Doctor Strange's nemesis, who would bring a pretty unique angle to things compared to the sci-fi-ish flavor of the Avengers movies.
The sky is the limit; not every villain needs to be as threatening as Thanos in order to make a compelling story. And they have decades of stories to pull from.
Unfortunately three of the most threatening villains in the Marvel Universe, Galactus, Annihilus and Doctor Doom, are tied up in the Fantastic Four rights.
