You, my friend, just hit the jackpot. I was about to edit my post with my Samus vs. Ganon analysis. Another top-contender is Mewtwo.
We have no way of knowing how Samus would deal with a high-level telekinetic or magical beings, as she's never encountered either (unless you count Nightmare as a telekinetic), nor do we know how Ganon would counter technology thousands of years before his time. Also, there's the question of whether or not the Light Beam would affect him the same way the Light Arrows do.
THEN, you have to wonder how powerful Mewtwo is compared to the rest of the cast. Obviously, he's toned down for fairness reasons, but he's the most powerful Pokemon among literal GODS.
Really, it's a three-way toss-up between Samus, Mewtwo, and Ganondorf, assuming there is no outside help (so Pit cannot use Palutena's Power of Flight).