This is the same type of debate that fighting games get when it's controller vs. fight stick. It's simply a preference, as you can play both ways optimally depending on your style. There are some advantages over others (healing is significantly easier on kb with mouse macros vs. a controller cycling through the party list), but the game was designed around ease of access on both accounts. I always tell new players to enjoy whichever comes more natural to them.

Personally, I'm a controller user. I have been since FFXI, and I love the immersion I get from playing with one.