First off, I would like to thank Crytek for giving Crysis 3 such a good story. So many loose ends from Crysis 1 and 2 are tied up in 3. That being said, however...

How did Prophet replace his Nanosuit 1.0 with 2.0?
How did Prophet ensure that he would regain control after the suit bonded with Alcatraz?

AFAIK Prophet was in the NS2 program where Crynet gave him the NS2
Alcratraz basically turned into Prophet. I don't exactly understand what you mean by the second question

First off, I would like to thank Crytek for giving Crysis 3 such a good story. So many loose ends from Crysis 1 and 2 are tied up in 3. That being said, however...

How did Prophet replace his Nanosuit 1.0 with 2.0?
How did Prophet ensure that he would regain control after the suit bonded with Alcatraz?

Give thanks to Steven, he was the C3 writer and a cool guy.

Those 2 questions are just impossible to answer, in fact the more you collect data about the first one the more more plot holes you will find.