- The first movie is very ambitious, you feel the ambition to tell a great story in the best possible way with the maximum of quality. If you watch the making of of "The Matrix" you will realise almost everything is 'hand made' no cgi characters or models (except one scene, where neo touches the mirror). All wirework and models. Alas, the other two movies were produced in one stroke and have tons of bad cgi in them. You don't get that same 'labor of love' feeling in the other two movies, imho. They come across as rush jobs with a lot of wasted potential starkly contrasting to the first film in that respect.
- The character of "Tank" (one of the few links to the first movie) was written out of the story and replaced by the jarjar-binks equivalent of that character. Just a lame rastaman stereotype put in there for comical relief "woohoo!".
- Zion. In the first film the only place you really get to see of the real world, is Morpheus' ship - the Nebucadneza. You get this eerie "Das Boot" feeling, with all the ragged cloth and the crap they have to eat. And then you have Tank talk about how cool a place to be Zion - the last city - is. But when we actually get to see Zion, it's nothing more but a huge gargantuan "Nebucadneza" - the people still wear rags, they don't even fix the holes in them. Only a few military folks are allowed to wear some old school star trek uniforms. I simply expected something new and wondrous instead of a tired steam-punked repetition of the 'Nebucadneza' design style.
- The elongated 'dance party' scene intercut with some mild adultery scenes. One of the few times I was truly bored in a film. The whole logic of "we are aboard a ship with a minimum crew and thus have all the privacy in the world - but we wait with sexuality until we arrive at a place were we can be sure that we won't get any privacy at all" didn't really make any sense to me. Heh, funny thing. I just noticed an interesting parallel: Anakin and Neo are both chosen ones and both dream of their loved ones dying.
- "Battletech" style defense vehicles, as with the whole Zion setting I didn't like those at all. Just showed the lack of ideas on behalf of the Wachovsky's, imho.
- Establishing the Merowingian as an important opponent/factor in the second movie and then abolishing that approach in the third film, by basically writing him (and any of his plot relevance) out of the story. Just another example that the Wachovsky's didn't seem to have any idea where to take the story and thus, what to do with that character in the third film.
- Replacing the deceased actress of "The Oracle" with a bad attempt of casting a 'look-alike' actress, instead of being bold and keeping true to the religous motives appearing in the film and using one of the kids (or potentials - as the oracle called them) as a replacement, thus following the logic of circularity of events.
- All in all failing to deliver original ways to show the power "the one" has within the matrix. It merely boiled down to: Ok, he can fly, kick ass with kung fu and see the code.
To me, the Matrix trilogy is a very good example how it is sometimes better to stop when you have to admit to yourself, you've run out of ideas that are as original as the initial ones. Lots of potential wasted, it's sad to me, since I'm basicly a fan of the first film and would have loved to see the story continue to be told in the same passionate way as the first one. I love the "Smith against Neo" coreplot throughout the trilogy, but everything else around it just doesn't strike a cord with me at all.