I finished Crysis 2 last night and I'm so confused with the ending! Did Alcatraz become Prophet as I swear it was Prophet's voice or did he just take Prophet's name or something like that?

What i think happened, was since an imprint of prophet was left in the suit, and alcatraz was basically dead, prophets conciousness took over

Alcatraz isn't dead. His body is just damaged beyond any help, which means that he would die >IF< he would leave his suit.
Since Prophet his conscious remains inside the suit, and he said at the beginning "They used to call me Prophet, remember me", Alcatraz probably changed his identity to Prophet to pay his respects to him.

I think that Propeht used the Nanosuit-Voice-Creator to answer Rasch's call because Alcatraz can't talk anymore because of his injuries. So jeah, Prophet is a second "AI" in the suit.

I think both Prophet and Alcatraz are alive in there.
Prophet keeps on saying "we" during the ending videos. "We're needed".

Certainly sounded like Prophet's consciousness made a resurgence. When you consider that Prophet has been talking to you through the suit on multiple occasions, and we have seen nothing of Alcatraz even attempting to speak, the only logical conclusion is that Prophet was the one speaking at the end.

On a more speculative note, the fact that Alcatraz's body is practically a cadaver, and that the suit is growing into him, it becomes arguably more likely that Prophet has/will take over.

EDIT: also, there was no indication whatsoever that Alcatraz's vocal cords were damaged in the body scan - at the start of the game the marines attributed his silence to him having too much tequila the night before.

I think that Alcatraz took the title of Prophet as he fullfilled everything that Prophet wanted to do.

Also note how the suit starts talking in a more human way over the course of the game. I just think the imprint of prophet on the suit is acting as kind of a second AI.

I don't think it's a second AI really, it's very much a 'living' prophet. The thing is the suit grows into you, developing the symbiotic relationship to keep you alive. In doing so, I suspect your body largely becomes a husk (comparable to the CEPH's exosuits really), with your conciousness moving to the deep levels of the nanosuit. This has already happened to prophet, and hence he was 'alive' within the suit in the same way that Alcatraz is alive. It seems that over the course of the game you go through several processes that adapt the suit to yourself, especially given that the alien spores are captured within the suit and re-released in a modified form. The last extreme dose of spores probably changed the suit dramatically, and this possibly allowed prophet to become a present consciousness within the suit. Rather than a deep-level process.

I agree with the person who said that Prophet's consciousness is like a second AI in the suit. The story seems to be about getting us to wonder what about Alcatraz is human and what isn't. If Prophet now resembles another AI (and therefore represents Alcatraz's new mind), the mind, body and technology components of Alcatraz are effectively separate entities. Alcatraz has a body that can occupy the suit, but he has no idea what he's supposed to do with it. Prophet has those answers, but he no longer has a body with which he can occupy his suit. And, as has been made abundantly clear by the game proper, the technology (nanosuit) makes the Alcatraz/Prophet, body/mind combo into a viable tool. It links the two and empowers them both as a single unit. But, of course, the suit would just be a fancy coat rack decoration without a body and mind to occupy it.

In Crysis 3, then, the writer would be able to explore the boundaries separating a man's body, his mind, and the machine that augments his humanity. They'd be able to take the transhumanist messages of Crysis 2 a step forward, examining body/mind/technology symbiosis rather than the simpler man/machine symbiosis examined in Crysis 2.