So what should have been done differently? All of the team listened to Captain America, even Stark. Cap told them what to do, planned the fight, etc. He's clearly the leader, right? Originally, Rogers was the central character that the film focused on. But would that have made the film better instead of just being a straight forward ensemble? I'm not so sure.
Stark gets the missile "sacrifice" at the end, sure (he's also the only one that can fly, save for Thor), but Rogers gets that moment of taking the war in when he walks out into the city after having saved all those civilians. No other character gets that. He's the first one to really "sign up" and go after Loki, alone. I think he has just as many moments as Stark when I really think about it. Neither of them win the rivalry they have going on between each other, both of them have interesting plot threads that they follow.
Yeah, there's clearly a preference for Iron Man in Avengers, but he was technically the first in this film universe. He's also the most showy and extroverted so it makes sense that Cap would be more quiet and subtle compared to him. Those are the characters. Compare Rogers first appearance with the punching bag to Stark with Potts and Coulson. Those introductions pretty much speak to their characteristics. I'd have loved if the film focused on Rogers perspective as it was originally intended, but I don't think that would have been right for what they were trying to achieve. Whendon loves Iron Man, but if he didn't care about Cap, I doubt we would have gotten the scenes we did in Avengers. They certainly wouldn't have wasted their time filming this,
I guess what I'm saying is, I don't think Captain America was given a disservice in Avengers. It felt appropriate. I also don't think we'll have to worry about this sort of thing in the long run from what we've seen with AoU and what Civil War entails. RDJ/Iron Man will always have the edge since he was the "first" and is so ostentatious, but think about it, that has it's drawbacks. I really think they're going to set up Stark as the unlikeable one, if he isn't already there.