Dust: An Elysian Tail, one of the few highlights of this year's Summer of Arcade, actually had to cut a major chunk of its story to make release. Speaking with Gamasutra, Dust co-writer Alex Kain says they had to cut a third of the game.
Creator Dean Dodrill's original vision for Dust had "a massive third act," according to Kain, taking players to new locations, with a new main antagonist and refocused storyline. This would have required months more time the team didn't have, so it was cut.
Kain says, "It was hard to part with the mysterious final villain, but the game ended up a lot tighter, and the story felt much more satisfying ending where it did." Gamasutra has much more on Dust in its extensive postmortem.