I've yet to try an FPS on the iPhone or iPad, but as an avid former Q3 player, I can't imagine the controls working. At all.
I think the original Quake--and also Unreal--would be fine on the iPad. Both DOOM and Wolf3D have a control scheme that can be customized based on your own preferences, and I think both games run well on the iPhone. They also run well on my iPad, but of course they are pixelated at 2x resolution. Considering that the games were pretty pixelated to begin with, it's hardly noticeable!
;)