I think it really all depends on the feel your going for. The control scheme should exist in harmony with your art style and sound style. Mouse based controls feel more modern - like a cheap conversion of a fps whereas keyboard controls gives a more retro feel. I didn't bother to read everyone's posts so someone may have mentioned this already. But anyways, thats what i think.
Let me explain better about my game:
In my game you don't play alone, you are a captain and you can control your soldiers. In the past month I made the AI for the game, and I'm very proud about it (there are four levels: Patrol, Follow, defend and War AI). But now I have to decide how the shooting engine should be. The game is kind of Operation Flashpoint 2D, a small sized conflict (based on the serbian war) that is separated in missions. I hope you guys understand this and I hope to read some good opinions. Thanks