According to Captain America: Civil War's writers and directors, the Marvel Creative Committee wanted to cut the film's climactic fight between Captain America and Iron Man.
These and other revelations are featured in the newly-published book The Story of Marvel Studios: The Making of the Marvel Cinematic Universe. For the uninitiated, the Marvel Creative Committee -- which consisted of Marvel Entertainment CEO Ike Perlmutter, president Alan Fine, Marvel Comics writer Brian Michael Bendis, Marvel Comics publisher Dan Buckley, and Marvel Entertainment CCO Joe Quesada -- oversaw the creative process on Marvel Studios' films until 2015, at which point Marvel Studios' Kevin Feige began reporting directly to Walt Disney Studios chairman Alan Horn.
Civil War famously ends with Steve Rogers and Tony Stark coming to blows after Tony discovers Bucky Barnes not only murdered his parents (while brainwashed and serving Hydra as the Winter Soldier, that is) but that Steve knew about this and kept it secret. However, as detailed in The Story of Marvel Studios, the Marvel Creative Committee wanted to drop this emotional climax in favor of having the film's heroes team up to battle the other super soldiers in Hydra's Siberian facility. "We had to do a draft where they had a fight in a submarine base with five super soldiers," noted co-writer Stephen McFeely.
"We kept saying, 'There's nothing interesting about that film. We're not here to make that movie. We're not interested in telling another superhero story," said co-director Joe Russo. When Feige sided firmly with the movie's creatives, it started what Russo called "a civil war in Marvel. But when we drew the line in the sand, it became a moment where that company was either going to slowly bend back toward where it had come from, or it was gonna slowly start to bend toward new territory."
In the end, Horn brought everyone together to argue in favor of their preferred ending to Civil War, with the film's writers and directors ultimately winning out over the Marvel Creative Committee. This was also one of the key events that paved the way to Marvel's restructuring, resulting in Feige and Marvel Studios no longer having to answer to the committee.
Source: The Story of Marvel Studios: The Making of the Marvel Cinematic Universe, via /Film