I'd like to see Thor relate most to Stark, since their worlds are very much the same. Both are gods (one metaphysical and one financial) both are sons living in the shadow of their prestigious fathers, both filled with paternal angst, both spoiled rich kids who are stripped of their privileged status and thrown down from their pedastals. They really have a similar arc, only IM has Thor lapped by one, and it would be cool if Tony sees through Thor's divine bull***** and call him on it, and then kind of mentors him when the others aren't around.
Meantime, I see Cap becoming buddies with Hawkeye. Their both SHIELD agents, both skilled soldiers and both regular guys on the inside. I think Hawkeye could be his touchstone in this new world. Clint could be a little in awe of the first Super Soldier, and he'd be the one to 'babysit' Cap. I'd love to see him bunking with Rogers, explaining aspects of modern living like cell phones, chinese take-out, internet porn, reality tv, modern weaponry and the like.
Of course Steve and Tony will butt heads and ideaologies. I'd be dissappointed if that continues past the end of the second act. The third act turn should ramp up the immediacy of the threat that all the bravado and ego flexing comes to a halt. Its also at this point that Iron Man realizes he doesn't have the emotional stability or strategic mind to take the lead, and without fanfare turns to Cap and asks for orders. RDJ can convey Tony's mind in a contemplative stare, a dart of the eyes, and that's all this would require. To see him make up his mind, unflinching and without remorse as Stark always does, and then turn to Rogers and be real with him for the first time in the film would be fantastic.
And Cap should be completely overwhelmed by Widow's empoweredness and overt sexuality. There was nothing from his timeperiod to prepare him for that! I think some great comedic moments could be found in their interactions. Don't have to dwell on it, but it could be used occasionally to punch up a scene.