Well after "Thor" pretty much cleaned house by himself against Captain Americas team, I would say Iron Mans side would win. But I doubt they'll use Thor again for sometime. Also some people on Caps side just walked away from it all. So its to close to call at the moment.I doubt Reed Richards will switch sides. They'll probably disband the Fantastic Four for a stint. We'll have to see if Dr. Strange, the Hulk, or the Silver Surfer side with anyone. Anyone of those guys would quickly turn the tide.
I doubt the new Thunderbolts will do much damage. Its strange that most of them are villians who go against people that are on Iron Mans team. Mainly Spider-Man. So Spidey seeing all his foes will most likely cause him to join the Cap.