Trelve posted... Not him but maybe it's the way the game lies to you to get it's stupid twist to work. It's not technically the ending but it annoyed me all the same. It serves no purpose other to have a twist for the sake of it. Zero Time Dilemma has a similarly stupid twist ending and I'm surprised its not been mentioned.
Ehh, I don't mind that aspect, personally.
There are a lot of plot points in the game that strictly wouldn't work if you had a linear story. I can understand feeling like the twist is a bit cheap, since yeah, the game DOES lie to you, but I understand why they did it. I think it ultimately enhanced the game, even if I can admit that it is a bit cheap.