I saw this today at a matinae, I really enjoyed it. The film ended the way I had a feeling it would. Not much was explained at the end, I believe the Wachowski brothers did this on purpose; they most likely wanted the viewer to draw their own conclusions from watching the film. Much like with religion, all the answers are not known, you must derive your own interpretations from the information which is given and known.
I think this film, much like Reloaded will polarize viewers. Some will love, like, or hate it. The ones who will hate it are the ones who go into the film expecting all the answers to be revealed on a shiny platter. I here to tell that not everything is explained, but what is giving should be sufficient enough for you to connect dots and draw your own conclusions.
To me the Matrix trilogy ultimatly boils down to four things, choice, purpose, love, faith/belief, and sacrifice.