Last generation...
Well... to determine a winner here, you only need to look at last generation's Godzilla versus King Kong.
Donkey Kong will want it more, but he just doesn't hav the means to beat the King of the Koopas™. There are only so many barrels you can throw.
To further prove my point, I played Super Smash Bros. Melee and put both characters on level 9, and had 99 men for each, and Bowser won with 16 men remaining.
I rest my case.
bowser can teleport, jump extremely high, run very fast (but has a hard time turning), deadly firebreath, is heave and wellprotected, and do i need to mention his brute force?
still, donkey kong wins. he is generally accepted as the most powerful fighter of the mainstream mariocharacters. he is too fast for bowser and would punch him hard in the face or something so he cant walk anymore.