Putting notably different 'mons like MewTwo worked, since he could talk and engage in pugilism with Ganondorf without distress. Jigglypuff is absurd enough to be fine, Pikachu is too iconic not to be in the game. Pokémon Trainer worked since he represented something greater than just a 'mon. Lucario seemed a little strange, but works fine I guess.
If they put like, a Garbador as a playable character, that's where I take issue with it. Now it just seems out of place. And not in the comical Jigglypuff way either, since (s)he's been permanently grandfathered into the series by virtue of being in the first one.