*How about a cheat code for realistic car deformation, now that we have real-time damage, wouldn't it be awesome (not on missions) to hit a wall at 50mph and completely obliterate the engine bay!
*Another cheat that lets us drive trains OFF the tracks and through the streets, complete with steering
*When other people get too close to the player, you can't shoot them, this gets annoying, especially when they're shooting you!
*Baseball bat is glitchy at best, when the other person is on the ground, you can't seem to hit them very often
Bring Back (just to reiterate what everyone else has already said):
*Planes, trains, and .. automobiles?
*Awesome weapon variety of Vice City and San Andreas