User blog comment:AdamGregory03/Bowser vs. Ganondorf/@comment-70.30.33.106-20141015070351

This is actually a surprisingly close fight. Ganondorf's triforce of power would greatly help compare his strength to the dinosaur, and Bowser is actually a much smarter villain than you would think. On top of that, both are magic users who uses it to amplify their own power even further.

The deciding factor is competency. With all his power, Bowser has had nothing to show for it as he's constantly been bester by a smaller, weaker, and arguably less intelligent and agile foe. Ganondorf, on the other hand, had managed to rule over Hyrule for 7 years, conquered it again a century later, and couldn't even be drowned by the gods themselves. Damn, Ganondorf would've made a great plumber.