I'm one of the few who plays with my mouse inverted and just one problem in the single-player (which was also present in Crysis 2) is that during the in-game cutscenes and the part where you shoot down gunships in the VTOL, the mouse y-axis always reverts to normal.
Not a big problem for the cutscenes as you aren't moving around the camera much but in the VTOL mission it gets confusing and difficult to aim. If you play without the inverted y-axis, just try turning on invert a bit and shoot some people. It'll drive you nuts.
It's a small problem for a small few but I'm just putting it out there. As for the game, enjoying it all around.