Well I generally enjoyed Prototype.
The boss fights were pretty weak though, you can cheap most of them with whipfist if you really feel like it...
The whole stealth aspect was cool but sometimes it makes no sense. You fall from 300ft disguised as a marine, landing in the middle of a base and the soldiers are all like "wow, cool, how'd you do that?" then just go on their merry way...
I did like the web of intrigue, but besides that the story was basically "protect your sister and figure out what's going on."
The powers were easily the best aspect of the game, being able to shapeshift on the fly and take on whole armies with any of your abilities was the most enjoying part of the game.
I wish that the concept of destroying bases/hives had more of an impact on the flow of the game.
Knock out a couple military bases early an the infection goes on a rampage, or unofficially side with the military and drive the infection back. This could have incorporated a number of different endings and would have given the game more replay value.