I've found that if I modify my keybindings, I can't exit from the weapon customization screen. If I have it mapped to the default X, I can press X again to exit. I'm a lefty, so I typically use the number pad instead of WASD, and I like to use Page Down for the weapon customization screen. It works to get into the screen, but then nothing works to get out. I have to hit ESC to pause the game, and again to return to the game, at which point it exits the WC menu. This is not game-stopping, but it is kind of a pain in the ass.
Also, as has been reported before, hacking doesn't remap to the Activate/Interact key, but rather stays as F. Again, not the end of the world, but it svcks to have to jump over to the far side of the keyboard instead of using my remapped keys.
Otherwise, great game so far.
EDIT: Oh, also changing seats in vehicles can't use the same button as Crouch if they've been remapped, even though both use C by default. These things all worked properly in Crysis 2, so hopefully they can be corrected in the first patch.