1) Morpheus is Alive (he never died, but used known cloning techniques to fake his death for the Merovingian's Assassin)
2) Neo is not dead--sorta.  His RSI has been recreated possibly as Sarah Edmontons and he has no memory. So he may as well be dead... Unless we get to pull a Star Trek 3.
3) The Red Eyed agents are parts of Neo looking for Neo's new RSI.  (Notice their Eyes are burned out... like Neo's from Movie 3)
4) Morpheus is in hiding with the Masked Men.  He needed a safe place to jack in since he is suppsed to be dead and he is using them.
5) Masked men dont want to become batteries, that is just what they say to the public.
6) Niobe will probably end up being foolish and getting herself killed.
7) Morpheus will come out of hiding when this happens.
8) The Assassin is a female.