I think Caps motivations were understandable--I think the movie itself would have be helped though by a little more connective tissue to the source of his concerns. In the movie, you essentially had Cap starting to talk to Tony and possibly signing, then Wanda being held on base was what made him freak out...That scene felt very flat, Tony's reaction felt unreasonable--she worked with a known terrorist organization, the same one that brought down SHIELD, and she's not a U.S. citizen. People died in a foreign operation she was on, it's pretty reasonable she stays in the compound until things settle down.
In any case, I was watching Winter Soldier against last night..And the scene came up where Nick Fury talks about potentially salvaging some of the Carriers--and Steve says no way, the price for them risking everyone and Hydra growing under the organizations nose was it all goes, it all ends. This is the one problem I have with Caps logic--if ignorance towards an internal threat is justification enough to absolve an organization? Then why the hell is he pushing for the Avengers to remain after Ultron? Ultron grew right under his nose, after all. Yeah, Tony didn't tell him, but that's because the Avengers are compartmentalized; exactly the reason he said Shield had to go.
So his ideological reason for not agreeing to have the Avengers change? Felt a bit weak during the mid film crisis, understandable, but a little weak--I think some specific catalyzing event connecting to WS, like Tony's guilt trip scene, but for Cap? Would have been better. (By the end of the film I actually felt that Cap's motivations were fine, though--because the organization trying to control him had allowed Bucky to be tampered with, illustrating the same weakness shield fell too. But the mid movie choice felt pretty week, especially how he didn't trust Tony with his hunch.)
But overall, that's a small gripe, as said, anyone can easily fill in the blanks based on, as you said, Winter Soldier.
