Re: Robert Redford offically joins Cap:TWS
My theory is this;
Fury gets away with his actions in The Avengers, but he had earned the displeasure of the WSC. At that start of the movie, SHIELD fails at preventing a terrorist attack or the like (possibly the events of Iron Man 3), so they use that as cause to retire Fury. Pierce replaces him.
Cap had left SHIELD after the Avengers out of outrage at the phase 2 weapons. Redford recruits Cap back, promising him he'll run a different kind of ship.
Cap ends up finding out Pierce is far worse than Fury.