To get a little off topic, if it's a strict Mouse/KB vs Controller, it really comes down to personal preference. I've heard my fair share of how using a mouse and keyboard is FAR superior when it comes to First Person Shooters, and vice versa. However, whenever I play Battlefield 3, or Black Ops 2 on PC, I regularly get first place or top of the board using either. It's all about what you feel comfortable with, as someone else said they feel more "at home" with a controller. Depending on what you grew up with, or what you were mainly into, one might just feel better then the other. Sure, a mouse can sometimes be more helpful in getting a much more precise movement, but if you've used a controller long enough, that can do the same thing.
In a vice versa again, I've played my fair share of Console Games with a mouse and keyboard using something called the XIM3. Emulates full controller support with a mouse and keyboard.
However, a controller is inherently better when playing certain types of games like Fighting or Racing. While Mouse/Keyboard is of course entirely better for RTS games.