I'll just get straight to the point:

Open Steam Library -> Right click on Prototype 2 -> Properties -> Local Files tab -> click Browse Local Files -> Right click prototype2.exe (the one with the Heller icon) -> Properties -> Compatibility tab -> check Disable fullscreen optimizations and Run this program as an administrator -> Click OK

I wasn't able to run the game at all, had a black screen and was forced to quit the game with the task manager, until I did this simple step. Fullscreen "optimizations" are a horrible thing in Windows 10 that's designed to make all fullscreen programs (like games) run in a sort of hybrid fullscreen/windowed mode so Windows notifications can appear over the game window, but it introduces all sorts of problems and even reduces performance in some games. I'd recommend disabling the optimizations on any game you're having issues with, just to see if it fixes them.