Halo 2 PC felt better with a controller because it featured huge autoaim when you switched to a controller. I assume M/KB will feel fine if they remove that.
lol, no, the autoaim had nothing to do with it. Could get kills just fine on both. It just feels better, especially for combined inputs and trick inputs which you are constantly doing with both of your hands at most times. Not even talking about the aiming or putting shots on target here, more "everything else".
Same reason people tend to prefer gamepads and fightpad for PC versions of fighters.