Don't read this if you haven't seen it yet!

Zion is another level of Matrix and everyone in any Matrix is a program...

While I seem to be the one person on the planet who wouldn't mind the "matrix within a matrix" answer, I really don't think that's where this is going. It makes sense, but it's also been done before (the 13th floor for an immediate example, which came out around the same time as the first Matrix). Anyway, it's probably intented that we think it's a matrix within a matrix right now (after the second movie), but it would really bring the first movie down a few levels if "reality" turned out to be a hoax.

[One theory is that] The whole point of the Matrix is to find the one program that is a true human AI.

If my theory of "love is the answer" turns out to be correct (and I think it will looking back at the climax in both movies) the "search for the real human AI" probably wouldn't work unless both Trinity and Neo are involved (since their love seems to be a focal point).

But if Neo can shoot lightning bolts and programs can leave the Matrix, then things are going to be pretty disappointing.

I have no problem with programs leaving the Matrix. Smith has just managed to reprogram a human beings brain (this also happens in the 13th floor). As for Neo's powers at the end, I'm hoping there is some other explanation other than "he suddently developed psi powers" because that would really irritate me. I don't have any other answer though.