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The only real problem with customizing your controls is that if you aren't playing on your system, you might forget to change your controls, or you might not have time to. I suffered a lot playing Halo one time because I kept switching off with a guy who had his controls completely inverted, and...

Oh THANK GOD we can use the old Gamecube controls. I haven't gotten a chance to pick up a Gamecube controller yet so I'm using the Wii remote/nunchuk combo. I used to use the X/Y buttons on the cube controller to do all my jumping. I'm having the hardest time getting used to my jump button...