That they made it unsympathetic in Reloaded. If in the end they added a ending that when Neo walked out of the Architect room that Zion was instantly destroyed, gruesome death scenes included, I absolutely would have not given a fuck. The characters in Zion were cookie sheet cutouts, the rave scene was excessive and laugh out loud bad(it seemed a 50 year olds idea of what happens when teens party). For being the last human city I just really felt nothing for them.

Its only in Revolutions, with the battle scenes of them fighting the losing battle that you begin to feel anything for the characters. Their will to live made them human, because the scenes in the previous movie where they showed the tension and day to day life that they lived failed to make them anything remotely that an average filmgoer can relate to. Thats why Oz and Zee's role you can easily do away with. I mean Tank's one little three sentence speech on Zion in the first Matrix movie made me feel more for the city, then the 30+ minutes they dedicated to it in Reloaded.

Now, as far as the biblical, philosophical ideas the Matrix throws at you I think im in the middle of the pack. I don't think its a total bullshit copout like some of the detractors of the movies, by the same token I don't buy the 'Its really REALLY deep' idea that some of the fans propose. Because, once again, it failed in Reloaded for the most part. The little speeches where they attempted to drive the point home(well, in the Merovingaian(sp) and the Architect's case to provide a counter-argument) absolutely sucked and were self indulgent. The philosphies that the Matrix hinted at worked best when they weren't blatant hammer on the head messages, like the oracles appearace in all three films, or Neo meeting the program family in the beginning of Revolutions. Moments like when they blinded Neo and now 'he can see' with the blatant zillion biblical and philosophical ideas that it represented made me cringe. Moments when the father program pointed out that "Love is just a word" made me smile.

The reason why the beneath the surface idea's worked in the Matrix is that they were hinted at and nudged at for you to draw you own concusions. Something the brothers forgot alot of the time with the sequels. Its why imho, those movies fail as anything but straight action movies.