4. The Matrix: Path of Neo
Whether or not the ending of The Matrix Revolutions was a big steamy pile of cow dung is a debate for another time, but it certainly made a lot more sense than the ending of this game did. After the storyline pretty much plays out like it did across all three films, the climax of Path of Neo involved us being talked to by digital versions of the Wachowski brothers, who told us that the ending of the films simply didn't make sense for the ending of a game. So they changed it totally, and what happened was completely bonkers, even for the people who made the Matrix.
Original Ending After the digital dudes tell us that the movie's ending ain't gonna happen, we see the army of Agent Smith clones who have taken over the Matrix all meld together with loads of metal to create GIANT AGENT SMITH. This mysterious entity then picks up a pair of sunglasses from a nearby advertising board and puts them on. Neo must then dodge rocks and stuff to stop the giant Agent and destroy it into tiny little pieces.
Alternate Ending There was nothing wrong with keeping the movie's ending. Neo should have still fought against Agent Smith in the way he did in the film - there's simply no need for a giant ridiculous final boss fight in a game if the rest of it is done well.
Alternate Alternate Ending After defeating Giant Agent Smith, ten more Giant Agent Smith's invade Neo's space and he must dodge more rocks and destroy more giants into little pieces. This process continues for all eternity, effectively distracting the machines in the outside world enough that the humans can all run away and hide somewhere. Meanwhile, the Architect and Oracle do a little dance, make a little love, and get down tonight.