Neo may have survived, if he did the matrix has been rebooted so there will be the seventh Neo (as the Arcitect says this is the sixth version of the matrix.) So Neo (Tom Andersion, Reeves version) is reinsterted as a a Smith style agent to battle the new 'One.' I got this idea awhile back, I back it up with the fact that the comics say that the Maruvinjian (French guy, not good at spelling) is a previous 'The One' He has been reinserted as this character, why cant Neo be instered as my version?
Anyway, Zion wouldnt have the tech, Bane cut himself to bits and they didnt do anything about it. The Machines on the other hand may have been able to rebuild him.