Whilst playing the game, I believe at least a handful of us got the feeling that "Oh, I'd faint if this happened", but it wasn't ever done (or could've been done to a much larger degree). Got any of those, post them. Who knows, maybe they'll show up in a new game or in a mod.
Mine:
Item control
I would've just loved to see this being used more. Be it key items or just random debris. If something randomly shoves your item away as you hold it, I'd run and cry. It doesn't even have to be much, even just moving it a bit in any direction (even without losing control of it) would make bolt for the door.
Picture warping
I would've loved to see these changes to a higher degree. Imagine if Alexanders picture warped as you saw it, with his eyes going red (well that's clique, but you get the idea) one or two points in the game when nothing else is going on.