Actually, I find most things you do in Just Cause 2 are easier with the controller...about the only exception is shooting things. Doing hookshots off high buildings, though? Controller all the way.
I actually wonder where the almost-hatred you hear for console controllers from some PC gamers comes from. They seem to forget that you couldn't actually play the original Doom (or Quake, for that matter) with a mouse unless you used some strange and arcane console commands, and that a joystick was a necessary peripheral for PC gaming for ages--heck, you couldn't play TIE Fighter without one, it didn't give you the option! As I recall, the first "action" game I ever used a mouse for was Quake 2, which was, what, 1997?