I've said it many times around here but I still maintain there's one really great movie buried in the two Matrix sequels.
The Andy Dufresne cut would excise:
1. The Rave (obviously) - it's not just the dancing that's an issue but Morpheus' pep talk is terrible and the Neo/Trinity to love scene...eesh.
2.
The Kid - IIRC he was kind of important in the video game and they tried to cross over the two media sources. It didn't work, he's annoying as hell.
3. Persephone - as sexy as Bellucci is her "Vampire" stealing a kiss scene is just dumb. As is the two guys she shoots that are supposed to be "werewolves". They try to tie back to what The Oracle is alluding to earlier - it doesn't work. Just skip to her freezing the Keymaster
3. The forced love triangle with Morpheus, Niobe, and Lock. In fact, remove everything you possibly can with Lock. He's terrible.
4. Excise the Club Hel fight scene. Who gives a **** if they're upside down?
5. Remove Zee entirely. Her bitching at Link is tiresome and her battle scenes are totally unnecessary.
There's more, but that's of the to of my head.