Its spelled with an E. You were right the first time.
a. It is pretty obvious that Neo is gone. I'd put money on it. Neo and Smith annihilated eachother like an atom of hydrogen and anti-hydrogen colliding.
b. The machines REALLY have no need for humans... especially since it was shown that the sun still shines and the IDIOT machines didn't think to build solar collectors above the cloud cover. I think that they're sincere in seeing that while they could kill off humanity at will(as stated by the architect and oracle), they will not because The Source and Neo made an agreement and because of the fact stated above.
c. Disconnection from the Matrix will not happen instantly of course. I imagine that now that resources and effort aren't being diverted to controlling inhabitants of Zion, the humans and the machines can work together to help clear up the sky and possibly salvage what is left of the ecosystem. In any case, the Matrix now will probably serve as a buffer to 'come home to' and relax when one is not helping rebuild a human city/terraforming.
d. The Christ analogies in the matrix are fairly obvious, but martyrdom isn't exclusive to Christianity. Keep that in mind. However, there are other ties to the bible simply because it is ingrained in Western Culture.
e. Neo's ability to see the machines stems from The Anomoly's connection with The Source. He is able to see everything connected to it; the machine race. It could be implied that he was able to see their 'souls,' however this goes out the window when he's able to see power conduits, connections etc... which clearly have none.
I liked the movie a lot. I like Reloaded a lot more now too. The action, while hard to follow at times due to waves of squiddy, was intense and satisfying. The 10 people I went with all left with a smile on their face.
Now what I want to know is where the Twins went? Did they just fly away at the end of Reloaded? The way they were hyping them prior to Reloaded's release, I thought they'd have a bigger part to play.
Overall I like the trilogy. Kind of a cross between Terminator, Dune, and Superman.