So many good things about the Matrix movies. For one, you could actually get into postulating all kinds of theories and the movies would support a lot of ideas, unlike most movies that either have way too many plot holes or ones that never even try to have believable plots and make fun of you if you tried (I'm looking at Grindhouse & Shoot Em Up).
*SPOILER*
For instance, at the end of the third movie, when Neo finally kills agent Smith, there are many good theories as to why Neo won at that point. Obviously, it appears we see the machines "power him up", but an even better postulate was my friend's idea that when Smith killed Neo, he destroyed his own purpose and thus allowed Neo to win (Smith had previously made a grandiose speech all about the importance of their purposes, his being to kill Neo).
Not to say there weren't oddities I found absurd, such as the fact that Neo could rip poles out of cement, but if a door was locked, they were all like "Oh noes! We have to find another way! I can't break a door!" And I'll agree that he did fly away way too much latter on, though I personally still liked the shift into a superhero movie even if most people didn't.
You know it's a movie that makes you think though when Neo gets to the infamous Lobby scene and I lean over to ask that if this world is a program, are the security team that are trying to stop Neo are a firewall or more of a proxy (only to hear the groans of everyone who makes no attempt to think during movies).
I also wish there had been a few small Bill and Ted jokes though, something like when they get in a phone booth, Neo winds his watch first, or there be a phone book with San Dimas written on it.