No, they never come out and say whether Neo is a machine or what. It seems to be hinted at, though, that he is at least partly from the machine world (the references to him coming from the Source, etc.).
I'd say he's dead...kinda. More like he became one with the Matrix. I honestly didn't notice a crucifix, though the religious symbolism of him as self-sacrificing savior would be obvious.
Like someone already said, the machines aren't releasing all the humans, only the ones that want out, which is a good deal for everyone involved. The machines keep their power source, which stays stable since all the disruptive elements are being let out, and the humans who want to be out in the real world get what they want.
Personally, I thought it is an excellent movie, and the ending is no exception. |