Well, here's how I did it.
I used Jigglypuff! Yes, the pink puffball is easy to knock out, but has the hardest move in the game, Rest. if you time it right, It can decimate the opponents. Straight away, use Rest twice to take out Giga Bowser. Rinse and repeat 3 times. If you're good/lucky you can manage this without losing a life (but be at high damage). Avoid trying Rest on Ganondorf, cos he can easily jump up and negate the attempt. Mewtwo is easier to take out this way, cos he has very little to counter Rest.
Try and avoid the pair, waiting for items to drop down, but you may be waiting a minute or two for something good. Especially, keep an eye out for Mines, Bob-ombs, Pokeballs (essential to watch out for, since both Ganondorf and Mewtwo with go for those ignoring all else, including yourself), and some long range weapons like the Beam Sword or Parasol (good luck getting a Home Run bat, I've never seen one).
Both Ganondorf and Mewtwo have extreme homing sickness (ie they follow you constantly), which makes them pretty stupid. Simply jump over the pair - 3 jumps or more will avoid Ganondorf's jumping attack, so jump 3 times before passing over their heads. Eventually, the items will come so use them!
It's a pretty cheap way, but hey, it worked for me.
