You mean in a Pokemon game. You can obviously main a Pokemon in Smash Bros.
But you can still main a Pokemon in a Pokemon game.
On-topic, I'd PROBABLY have said Venusaur years ago, but after learning of EVs and considering that I raised him to lv 100 with Rare Candies (I got him to a good level first, but I don't know if I maxed his EVs or not), I'm not so sure. So I couldn't be absolutely sure, but probably my lv. 100 Gardevoir (whom I spent hours getting the right Nature and Ability by hatching hundreds of Ralts), the only Pokemon from my lv 100 Ruby team which I chose the EVs for, the Nature for, the Ability for...I strategically decided it all. Heck, I even spent time giving it an Egg Move, which I'd never done before. And its moveset is pretty awesome.