Those were always my feeling son the series and yet I have been repeatedly assured that no, it was always supposed to be a triology and was even pitched that way, so...no idea. the first one does stand alone so well though that I prefer to pretend there never were any sequels.
It is true that it was pitched as a trilogy, but it was not greenlit as a trilogy. The second two bits weren't given the go ahead until after the success of the first one, meaning that it was rather dramatically altered (from what I've heard) in order to work as a standalone action film. Unfortunately, I think what that really means is that the Wachowskis pretty much stumbled upon the things that made the first film so great almost by accident. It's refreshingly efficient as a bit of storytelling, while they seem to be anything but when given free reign. But, fine, you wanted it to be a trilogy with an extended narrative filled with existential prattle and religious allegory. That, in and of itself, isn't a horrible thing. And I was so taken with the first (and, to a lesser extent, the second) film that I was in full fangirl mode by the time the sequels came out and would have happily gone along with it had it been done well. I can forgive the sequels for being cheesy a lot easier than I can forgive them for not realizing how smart they aren't. Which, to me, is the biggest problem with the second and third films. Writer/director duo given a ton of money and fighting WAY above their weight class. As shown by the fact that they have only directed one film since (which I'll leave nameless in case someone wants it) and it bombed spectacularly.
My biggest problem with the sequels is that I just didn't care about Zion. At all. The more time we spend there as viewers, the more sympathetic I became towards Joe Pantoliano's character in the first movie. I'd want fake steak, too. And, it must be said, but don't even get me started on Trinity. As a female fan of action movies, I've gotten used to the women on screen being reduced to incompetent ninnies. I don't like it, but I accept it as part of the genre of which I am otherwise so fond. If Trinity had only ever been a sycophantic admirer of her messianic boyfriend who ultimately martyrs herself for his cause, I doubt I would have noticed. But to have her turn into that after a first movie in which she is every bit his equal (well, maybe not every bit, as he is "the one," but darn close) was horribly disappointing.
/rant