Man, the ending was kinda epic.
Now I have a couple of questions:

1. Is Alcatraz dead?

2. Is Prophet really reincarnated?

3. How did the change in the owners of the suit happen?

4. Is Prophets corpse still there where Alcatraz begins his journey?

5. Will there be a Crysis 3 and if, will it be a sandbox and will it be on consoles?

1. Dont know if Alcatraz is dead. It is hinted at during crysis 2 that the team are Dead men wallking but that dosnt mean hes dead yet.
2. Think hes dead in physical form. The suit on the other hand seems to have held onto his memorys and patched them into the suit to fix things.
3 No idea, theres no hints at all in Crysis one about this.
4 Yeah
5 Probably pick off where crysis left of with Prophet going to the island before the neclear strike. He did diapaear for most of the campign in Crysis one after he was captured, only to return with a big ass weapon but with a damaged suit. The damaged suit could explain the new suit?

1.Nope but without the suit = dead

2.The deep layer of the suit is actually the conscious of the codename "Prophet"(memories,experiences,DNA etc.) so Alcatraz is now the new Prophet.(delivering the knowledge? about the aliens) so yes

3.I dunno

4.Maybe

5.Yes,Don't know about sandbox,I think yes