I agree. It could have been great. The third movie felt like someone other than the Wachowskis had written it. Here is my version of the film:
Same movie up until Trinity saves Neo from the Trainman. Then cut back to the club, and Smith enters. Merv looks him over and says something coy. Smith tries to copy himself to Merv and the Twins and Persephone, but can't because like Neo, Merv knows how to prevent copying. So Smith and Merv strike a deal to rule the matrix. Blah blah blah, the war continues as it did in the movie (with a little shorter battle, (less is more). Neo goes to the city and is blinded by Bane. Neo is ALL powerful against the machines, so there is no crash, no lame Trinity death, and so both Neo and Trinity go to the city. A deal is struck with the machines, who are afraid of Neo since they can't kill him. Neo is concerned about the people in the matrix, and what Smith is doing. He goes into the Matrix to fight smith, but has to deal with Merv and the guys. Neo ends up copying HIMself to fight everyone. Seeing this, Merv tries to betray Smith, but Persephone intervenes and ends up destroying herself and Merv, saying something like "its only a game..." So SUPER BURLY BRAWL comes in, with Neos fighting Smiths All DRAGONBALL Z style. Its a standoff, so Neo ends up sacrificing himself for the good of the people in the Matrix, and this allows Smith to be destroyed. Afterwords, Trinity gets some answers from the big daddy machine about what is going on and why Neo can see the gold light and how agent smith gets destroyed. The machines don't kill her because of the deal, and............The last line of the movie is something like "Trinity carries Neo inside her. Neo will live again." So! Trinity is pregnant, thus preserving Neo, and ensuring that the machines will not rise up against humanity. But what is to stop humanity from going against the machines? Well, nothing. But nothing would have stopped humanity from trying after Revolutions, anyway.
Yes, there are holes in this, but I think it is a lot more satisfying. Questions are answered that NEEDED answering, while leaving others unanswered, which is okay.