HAHAHAHAHAHAHAHAHAHAHAHAHA! Ganon wins, Giga Bowser is basically just a bigger Bowser, that's it.
Strength: Ganondorf is not as strong as GB, but Ganon is as strong or maybe more.
Speed: GB is much slower than Ganondorf, who as shown in WW and TP is very fast, and his ability to teleport only adds to this advantage.
Power: Ganon has massive magical power amplified by the ToP while GB has...fire breath. Whoopee.
Versatility: Ganon, by far.
Intelligence: Ganon, Bowser proves his idiocy every game he's in.
Ganon wins in a curbstomp. Bowser will always be the joke Nintendo villain.