I've switched to controllers when I can to avoid hand and shoulder pain. I've found that, ergonomics aside, which is better depends on the type of game you are playing. I'd agree that, mostly, mouse + keyboard is the superior input mechanism. But the 'WASD' bit fails when the controls require two analog inputs rather than 1 analog and one digital (driving games, flight sims).

I'm still looking for the 'best' controller though, as I don't think it exists yet. I don't know if you can combine a device like a mouse suitable for 'twitch' FPS games with controls suitable for a 6 degrees of freedom game like Descent, Elite or Star Citizen (which currently require two joysticks, pedals, and ideally voice control to play in 'advanced' mode).