MebeJedi: Actually after M2 I was struck with the same issue of the Sentinal zap. But, between that and the Architect's (painfully rambling speech) I was given the impression that M3 would reveal that Zion and the "Real World" (TRW) were another form of control (or more accurately the opposite side of the equation). That is, the TRW/Zion were ANOTHER Matrix, dirtier and less pleasant. If people rejected earlier Matrices because they were a paradise and you have a new Matrix MOST people find flawed enough to believe, you need to let the malcontents who see through it to think they've escaped by putting them in a tougher less pleasant place. Basically a prison in a prison. TRW would have a different set of rules than the main Matrix. Therefore The One would really be the person who discovered the second prison, found a way to bend IT'S rules and really free humanity from the machines. (There had to be a first who first freed themselves from the original Matrix why not a first who freed themselves from the Zion-Matrix.)

Re-listen to the Architect's speech at the end of M2. You can almost see what I just said.

If you ask me it would have been a much cooler turn out. Unfortunately, as much as I'm going to bend these movies to my will, there's just no way to make that story happen.

I'll just have to become a rich and powerful Hollywood producer/director and re-make the last film.

Edit: Ok, I think you talked me into it. I'm going to rework the script MeBeJedi. I had been living with the idea of Neo having TRW powers so long I forgot how much the idea blew when I first saw it. The Squid-zap is an easy cut. I was actually going to construct a new prophetic dream for M3 in which Neo forsees the upcoming battles, Trinity's death and his own blindness (if he can see the future, how did that take him by surprise?) At least that's an afternoon I'll have back.
Large cuts for removing BlindOVision should be easy enough, but the real problem is the real world Smith fight. If he's blind, how will he defeat him? I suppose he still know Kung Fu outside the Matrix. I guess it's easier to believe he's Zatoichi than Muadib.