I never understood why Donkey Kong did not have another character, namely Diddy Kong, in Melee as well. Honestly, I never thought that King K. Rool would make it on the main roster for Smash 4, but once DLC was announced, especially in regard to the poll, I had no doubts that the King K.Rool (I just started playing Donkey Kong 64 and never realized that his name could be pronounced as "cruel") would be playable.
I digress, I discerned the true reason for this discrepancy. King K. Rool is worth five or six characters because of how badass he is. So naturally, Sakurai did not want to include him because Donkey Kong, as a series, would be over-represented.