I think I have an identity for the mysterious 'Controller' in the Iron Man game.

If you have read any of the marvel comics then you may or may not know that Advanced Ideas Mechanics 'AIM' is lead by none other than MODOK, the guy with the giant head, for those who don't know.

In the comics he looks different to the game but has similar telekinetic and psychokinetic abilities. It may be him, but I'm not 100% sure, more like 95%.

Anyway, hope this helps you.:D