Let's face it: home video (mostly DVD) sales peaked in 2002-2004, and have been in a dive overall since then. That used to be the thing that made feature animation so profitable, and without that, unless you have a run-away-hit with lots of toys sold based on it, it's hard to make money with all of these animated films.
If there's a story change, they can't keep hundreds of people working while the thing gets re-written and new story reels are made, or else the budget just goes up too high to have a hope of a profitable movie.