There are a few things I was confused about in the movie:
1. What is the point of that Indian couple and their daughter (Sati) in the movie?? What happened to the parents? Why would they want to bring back their daughter to the Matrix but then not be with her?
2. When they are going back to the frenchman in that club, what are those gun-check dudes supposed to be? Why and how are they able to stand upside down??
3. I don't understand how Agent Smith is killed at the end of the movie?? And what is Agent Smith talking about how "this is the scene of the end...everything that has a beginning, has and end...this is a trick" I don't understand that.
4. If all of those people that were assimilated by Agent Smith (Sati, Saraphm, The Oracle) how are they brought back to life?
5. Is the ending implying a next movie? "...how long is this peace supposed to last?... as long as possible..."