So I realized the real reason why the Wii Fit Trainer is in the game... Clearly it was to shape up certain characters. Bowser and Yoshi now kick ass and don't slouch anymore. Bowser is like twice as fast as well.

Ike built his muscles up. Chrarizard can now fight for as long as he wants without getting tired. Not to mention good ole Ganon got a bit faster and stronger as well.

Seems the Wii Fit Trainer was mainly brought on to make sure everyone was in tip top shape.