Final Level: Project Impurity
Why It Sucked: For such an enormously ambitious experience to have no endgame play is totally unacceptable. You sacrifice yourself to save everyone, and that's it. The final cutscene's narration changes depending on your actions throughout the game, but all that is meaningless if there's no way to continue playing in a world that's been affected by your actions.
How We Would End It: Add some end-game content—the DLC expansions helped a lot, but they weren't exactly free. And this game needed another ending besides straight up martyrdom.