PT wouldn't work as a fighter because of Hal. When they were coming up with mascots to duke it out in SSB, they didn't think of a 11 year old to represent GameFreaks, they thought of the Pokemon themselves. Then with Melee, they further reinforced that it's all about Pikachu and friends. I like PT as much as anyone else, but now it'd be too late for him to branch out. It wouldn't look right.
"Why is PT fistfighting Pikachu?" would be on everyone's mind if he fought. If PT was part of the Original 12, it'd be different. With a racer coming out of nowhere with a Firebird possessed straight punch, and a pink fluffball that eats everything, he'd be in good company! Now...He'd be filler because there wasn't enough time to stuff in Deoxys or whatever, no matter how good he'd be.
Now instead of giving him his own movelist, why not expand on his current? As a pokemon trainer, he should have 6 pokemon. Now give those 6 Pokemon their own moveset. Take away Pokemon Change, the fatigue, and have the PKMN random set so you can't select your preference. Then it will be something fresh out of Pokemon Red/Blue! Pokemon Trainer vs Sonic would actually work! You may not be able to switch out, but you get six fighters for the price of one, and they can be normal, just like Pikachu.