*** SPOILER ALERT ***
A few notes before you continue on with this thread:
1) There *will* be spoilers
2) If you’re here to talk about how much you hated the movie, please take it to the appropriate thread
With that said, after viewing Reloaded I was left with as many questions as I went in with, so if you have a take on what happened in the movie, please post ‘em here.
My thoughts on a few things:
.=Zion=.
Two things that we know for sure at the end of the movie is that a) Neo stopped a sentinel while “outside” of the Matrix, and

Agent Smith is now in Zion. These two facts point to one thing: Zion is not the “real world” but is, in fact another portion of the Matrix.
.=The Coma=.
After stopping the sentinel Neo slips into a “coma”. I believe that Neo had a moment of ‘self realization’ when he did this that ‘blew his mind’, so to speak. If Zion is still technically within the Matrix, then it is very conceivable that Neo is AI and this realization caused a failure in his code. Or if he is human, it could be that this portion of the Matrix has a different security level in the code and since we’re still technically bound by the rules of the Matrix while within the Matrix, Neo’s realization causes a system error that boot’s him from the system. Either way I think that the coma is induced by code that is either a) written that way so if you “become aware” within this portion of the Matrix then you get kicked from the system, or

an error in the code that cannot handle self realization in this portion of the Matrix.
.=Zion Revisited=.
If Zion is still a part of the Matrix, or a different ‘security level’ then everything that entails getting to Zion (taking the red pill, breaking free, getting flushed, etc.) are part an elaborate program to convince these individuals that they are now free of the Matrix and are now in the “real world”. If this is the case then it is still entirely possible that everyone is AI and this is an attempt by the larger part of the system to “convince” these portions of the AI that they are, in fact human. If everyone is not AI, then it still makes sense to create an area like this to ‘contain’ these renegades that cannot be contained by the “level 1” version of the Matrix.
.=The Rave Scene=.
There are no gratuitous sex scenes in The Matrix, and I believe that this scene is imagery of a much larger event, that being the union of Neo and Trinity. Perhaps it is of major significance that their “code” merges, or perhaps it is important that we see that they are passionate for one another rather than assume that they are. If we never seem them “together” then we can only assume that they have been intimate, so I think that we’ll find out that it was important that they “merged”. This could actually be a huge point of the last movie.
.=Random Thoughts=.
If AI is written good enough it will not be able to comprehend that it is AI, as this is self defeating to a “pure” AI system. Is it possible that we are watching the creation of the first AI ever that Morpheus mentions in the first Matrix? Is this cycle of Zion a recompiling and running of new code to test the compassion level of the AI towards humans? Could it be that Neo, is in fact the purpose of the AI and the point is to create AI (Neo) that is 100% compassionate towards humans so as to advert world destruction. Did they run a simulation of the AI and deem that if left to its own devices that it would attempt to destroy humanity, so Neo is the “fine tuning” process to make AI “compassionate” towards humanity? The one “failing” of humanity, according to the Architect is hope, and Neo now has that...
I have more but my fingers are tired