I actually tried this (with XPadder) and yes, aiming was kinda hard. Especially getting a deadzone/sensitivity setting right for both quick turns and fine aiming was difficult. I used a pretty shitty pad (I think it has a certain bit of "hardcoded" deadzone) though so I think I might try this again with a PS3 controller.
Gamepad stick + left side dpad and buttons for different stuff crouch/prone/reload + mouse for aiming was awesome though.

Another approach to this could be a shared screen (perhaps zoomed a bit out) like in all them lego games.

I might try out this Xpadder program for myself. I havn't heard of it until now.