Legitimate Questions
All the ones with asterisks are property of Brad, not me.  Used with permission, of course, hehe.

-When an Agent takes over someone's body, do they die instantly?
-If no, where do they go?
-Do people get diseases in their pods in the real world which transfer to the digital selves, or are the diseases created by the Matrix?
-How do they make sure people look essentially the same in and out of the Matrix?
-Why do they bother?
-Does time pass the same way in the Matrix and the real world or no? *Note* I found an excerpt of a chat with the movie's writers/directors, Larry and Andy Wachowski, where it was said that Neo wakes up at 9:18 AM on September 18 (9/18).  However, at the end of the movie when he makes the phone call, it's logged as if it is still 9/18.  He spent ten hours in the real world in the construct (said by Tank), and he also slept and had several meals, indicating that at least a day went by.  So maybe this indicates some sort of time paradox.
-Is the Matrix version of 1999 altered from the real version which passed long before the Matrix was created?
-How exactly did they scorch the sky?
-Why do the machines allow wars in the Matrix? *
-Are the laws of physics basically the same inside the Matrix? *


                                  And the Rest...

-Do the foods taste as they should?  Or is that chicken soup really...tunafish?
-What version of Pentium is Smith running on?
-Or is he a....Mac?! (dum dum dum....*evil music from Brad*)
-To continue that, what computer company manufactured the AI? Boy did they ever mess up.
-How do you manufacture humans, and can it be done with ordinary household ingredients? *
-What version is the Matrix? 6.1? *
-Is the Matrix downloadable?*
-If yes, where can I pick one up?*
-Do they insure hovercarft in the real world? *
-Is Agent Smith a lawyer?  If no, how did they create AI that spineless? *
-Who came up with the brilliant idea to scorch the sky?  How did it work?  And did they really hurt whoever it was after?