The Matrix - After shooting the hell out of the lobby of the federal building, Neo and Trinity mount an elevator that was conspicuously silent in the original film. Decked out in their leather and wrap-arounds, the characters seem to have laid aside part of their humanity and have become more like the programs they are attempting to fight. What it lacks is a sense of creepy not-quite-normalcy that is found elsewhere in the characters' interactions with the Matrix. Instead of a quiet elevator, I would like to see "The Girl from Ipanema" playing as they enter the elevator. As a bonus, it doubles as an homage to The Blues Brothers.
The Dark Knight - The Joker pitted the good citizen commuters of Gotham against a boatload of convicted felons in a variant on the classic game theory problem, the Prisoner's Dilemma. Most people I've spoken to feel that even though ultimately everyone made the "right" choice - whether through moral strength or simple cowardice - it wasn't the "realistic" choice, especially for the citizens of Gotham. Though it fits with the moralistic and hopeful ending, the moralistic and hopeful ending seems out of synch with the rest of the story. One of the ferries should have gone down, and given the Joker's particular madness, it would have been far more likely that he would have lied about which trigger did what. There's one school of thought that thinks that the triggers should have blown both ships, but I want something less spectacular. I would have liked to have seen the commuters trip the switch, only to have their own ferry blow up. Then we're left with a boatload of felons who by all appearances blew up law abiding citizens and an angry city that would be screaming for their blood. That's the chaos the Joker was working for, and not the neat and tidy closure that we were given.