Can't be arsed to debunk most of your ****, but the fact of the matter is simple. All stories have improbabilities, ranging from LoTR to the Da vinci code. The job of a reader isn't to debunk a story, but to try and understand it. If a story becomes un-understandable, that's when there is plot holes.
Not to mention most of your 'plot holes' are based around information not given. That isn't a plot hole, that's called focus. There's a reason the LoTR trillogy didn't go into detail on what exactly happened afterwards to the remaining dwarves from the hobbit, because that wasn't the focus of the story, the same as what happened to Psycho wasn't the focus of what happened in Crysis 2, and why Alcatraz's training wasn't the focus of Crysis 1. Crysis 2 is about Prophet, NY, and Alcatraz.
Nanosuit 2.0 is overall more powerful, even ignoring the lore behind it (You're making the classic mistake/being a little bich, of mixing gameplay changes with lore changes), the ability to switch rapidly and adapt in combat. (Something the previous system would never allow) is far more useful then the ability to throw grenades far. (He can still punch through stuff, just there isn't really an abundance of flimsy Korean huts in the middle of NY, and Nanosuit 1.0 never said you could punch through solid brick/concrete (Which is what most of RL NY builds are made from). Not to mention it's a game. In all game storylines there is always a sacrifice between story and something looking cool. (For instance, how the hell did they keep hitting a island with a nuke 'Under wraps?' in crysis 1, there are limits to coverups). The fact is the new suit design looks cooler, and at the end of the day, that's all that really matters.
Overall it isn't that hard to piece together the story that's been told, and although there are unanswered questions, I very much doubt the stories finished yet.