The Melee Starting Video

[HulkSMASH]

But if Bowser were really a villain, he wouldn't play sports with Mario and be all fair with rules and stuff. Ganondorf would never do such with Link.

Like I said, Bowser's villainous flavor tends to change.  At his darkest like from Mario 64, or Sunshine, he's a match for Ganon, but when he's portrayed less seriously, like in the Paper Mario games, he'd get his ass kicked.