My view on some things. Hopefully it may help some to really appreciate the movie.
I believe that there is more to the story. The Indian dude at the start of Revolutions made reference to humans and the programs being quite the same. Intellect is the same, whether is it our biological brains or a series of ones and zeros. This is shown in a human emotion of love, he loves his wife and his daughter, yet he is not human. This aslo explains why the Smith program can be put into a real brain in the from of Bane (who's name is probably also symbolic).
Neo and Smith balence each other out, Smith mulitplying as Neo grows stronger. In the first movie this is not the case, however, as smith is just an obstacle. But when Smith gains some of Neo's ability when he is killed at the end of The Matrix, they become opposites. His only purpose is to kill Neo. Neo realises that this is the only way to be rid of him. If Smith's purpose is taken away, then he is deleted, much like the little Inidan girl, who has no purpose and was going to be deleted.
About the ending, I really liked it. The Rambo-ending would have been good, where the Humans beat the machines and free all the trapped humans, but this just takes them back to the beggining, as seen in Animatrix. They will just make the same mistake again, having to rely on machines. But with Neo's truce with the machines, to kill Neo in return for the war being stopped, its shows a new idea. People will have to live beside the machines. They will have to help each other out. Neo had no want to kill all the machines, just to stop the war. The machines and the humans realized that the way things were going was not thte answer to a good life. The programs will no longer enslave the humans and the humans will realise that the machines are just like them, just in different form. Remember too that the Oracle is indeed a program although she is a sentient life form too. She said to Neo during Reloaded, that she knew the only way forward for the two species was together...
That was mostly my words, but I've added some things from other people.
It is a new stage of human evolution.