very well put skyscream couldnt have said it better my self. Although My personal opinion is that morpheus is alive without any doubt. He is still alive.
In fact critical missions and local contact missions have said there is a place on the surface where people can jack in to the matrix. Also we there was a event because of this. Also remember that Morpheous after he was dead and his body was for up for viewing in the church in westview his body kept turning in to a swarm of flys.
Yes, Neo is still alive. We dont know if or how he is being held prisoner but he is. Morpheus said this in a meeting we had and also on a recording. Neo could be Sarah Edmontons but thats not confirmed yet.