I saw the movie YESTERDAY!! *hops up and down with joy* And here's my thoughts on it (after reading everybody elses).
The trilogy was just like any other rapture movie made, only it was made to appeal to a much larger crowd than the usual bible-thumper, as some people call us. Some people notice the religious overtones and go "whippie! a religious movie that rocks!" and some people don't care about it. They just want a cool action movie.
But it's just like the Lord of the Rings.
[religious mode]
The Matrix is our world, the "first dimension", as some might call it. It's a world created to be what everybody wants it to be, i.e. sunny and green. It's just like what the usual atheist believes the world is. But on the outside, the world is a war between the machines (devils) and the humans (angels) who are both trying to gain more people, either to use as energy, as a source, or to save.
Neo was made by the flaws of the Matrix, just like Jesus was made by the flaws of mankind. He was made to screw with the Matrix's mind and make things clear to everybody. He was made to save the world. Like God leading Jesus, Morpheus taught Neo this and trained him to do what he will, and like the Holy Ghost descending onto Christ during his baptism, Trinity came to make it official, to help save Neo so that he can save them. Hence her name, I do believe.
In the first movie, Neo dies and is resurrected, and Smith becomes seperate. He stands out in this world, just like the Anti-Christ. It is quite clear Neo's job to stop him, and so the big battle begins. Apocalypse.
In the second movie, Trinity is killed then resurrected herself. If you will note, in revelations it mentions a time when the holy ghost will leave the world. Although it's brief and vague, I believe it's symbolic because Neo brings her back. The belief in Christ will bring back the Ghost. It's the time of the seven year trials.
Then the machines start getting through to the city, sin has built up, and they are almost winning.
Then in the third movie, everything has been pretty much wrapped up except for the symbolism of Trinity dying for good. After the world has found true peace, then there is no need for the Holy Ghost. He might become an angel, or whatever. The same goes for Jesus. He will become God, and therefore, Jesus, himself, will no longer exist.
Even the ending was of God's choice to give mankind free will.
So the whole trilogy was the entire story of Christ and the revelations put together to make a good story.
I believe that it was done on purpose because it was even more vivid and there than the Lord of the Rings series, but I could be mistaken.
[end religious mode]
Seraph is a type of angel, BTW. Seraphim and Cherubim, remember?
Anyways, as for the movie itself, all the action and that stuff, it's very very cool and deep. I think that the Matrix movies are the most awesome movies I've seen, and that people that didn't understand the ending didn't understand God or know his story. And this idea has been proven many many times. Because if you didn't know God's story, you didn't realize the symbolism, and therefore, you wouldn't catch the story lying underneath.
As for the loose ends, I didn't really see any. The machines would draw their power from the sun after sucking in the clouds. However, I do believe they left room open for another movie or game or something.
And I tried to cover up the spoilers. Even though this thread is already dripping with them and the title has been changed as a warning, I think it's only polite.