There's also the fact that if you're playing with gaming mice, they often have their own sets of drivers wherein you can control the sensitivity to a much larger degree than the right analog stick. Skill level aside, a good mouse with proper settings will outstrip a controller.

From experience, I am far more accurate with a mouse than with a controller, though in part it is because I rarely play first person experiences (either shooters or RPGs like Oblivion) on a console. In the end, a mouse personally feels more natural when it comes to such games.