Excerpted from a dialogue between Ken Wilber and Larry Wachowski -- Ken Wilber passes on his own take on the Matrix trilogy and why people hate 2 and 3 so much.
As you know, I think it's incredibly gutsy because the whole key to the Matrix trilogy—this is my interpretation—is given in really in the last fifteen, twenty minutes of the third film; that the Rosetta Stone is when Neo, for example, is saying of the machines, "If you could only see them like I see em...they're all light. They're made of light", and so on...That interpretation is the key to all three of the films, and it's incredibly gutsy, because film number one—so many people sort of relate to film number one because it makes sense. You think it makes sense if you don't see the other two; it seems a very simple story if you look at just film one. It's very Manichean actually, which is, everything in the matrix is bad, everything outside of the matrix is good, everybody in the matrix is trapped, everybody outside of the matrix is free—and that very simple kind of dualistic thing—the machines are bad and they're trying to hurt freedom and so on. And so everybody goes “wow that's great!”
And then you go and you watch part two, and you get to the part where Neo's talking to the Oracle and says "you're not human are you?" She goes "no." He says "You're a program aren't you?" "Yeah." And everybody starts scratching their head, because now all of a sudden—and I've told you this, and again this is in my opinion—we're taken out of the realm of movie and into the realm of complex literature, because this is a very sophisticated plot now, with a whole lot of pieces, and a lot of the pieces of the puzzle aren't really given until that last part of the third film.
And that's where all of a sudden things really start to fall into place. They start to fall into place with the speech from the Architect, they start to fall into place actually with the first talk with the Oracle. Smith is a real key to all of this, and anyway, it's that overall interpretation, which is really that body, mind, and spirit appear in the Matrix trilogy, both in their alienated forms, and then in their resurrected, or healed, or more integrated forms, which happens towards the end of the third part. And that's why it's very confusing to some people if they don't get that overall big picture, that's why sorta part one makes sense and then they get lost a little bit in part two and part three.