I'm kinda miffed that they ended the movie by taking away Pepper's new powers.

Could've been interesting.

@Kikimaru
Very true. The "cure" Tony completed has drastic implications for the world of medicine.

Actually, like a lot of things in that movie, they leave that ambiguous. It either means "gone" or it means "Fixed the side effects"

Well, just like how it ends with Tony seems to retire from being Iron Man, but then as you recall back the movie, in the beginning he injects some mind-controlled setting for his armor, probably much healthier than that ark in his chest.