Honestly, I thought the movie did not live it up to all the hype. Here are my thoughts.
1. There is only one Matrix.
2. The sentinals DID NOT reach Zion. There was a battle fought in some access point. That is where the human "Agent Smith" used the EMP blast against the humans defenders.
3. It seems that Morphoeus skills have gotten weaker since the first film. He was barely able to dispatch that weak ass agent. I see a problem here.