If you guys want villains, a Pokemon trainer that fights for himself, and slight retention of those old Pokemon Trainer mechanics, why not Giovanni? His Down Special could work as a rotation mechanic where he starts his stock out by himself.
Summon Pokemon -> Withdraw Pokemon - Summon Second Pokemon -> Withdraw Second Pokemon -> Summon Third Pokemon -> Withdraw Third Pokemon
And so on and so forth. You'd have to perform your Down Special twice to switch from one Pokemon to another, and Giovanni is one of the only human Pokemon reps that wouldn't be useless without them. He could have a pretty straightforward team along the lines of Nidoking (bowser-y), Rhyhorn (as a mount / wario bike) and Machamp (little mac with faster attacks but lower damage per attack).
Only Giovanni's specials would use his Pokemon that's out. The tilts, smashes, etc. would remain the same. It'd also work kind of like Ice Climbers meets Pokemon Trainer with regards to stocks, where you have to take out Giovanni for it to count as a KO, but if one of his Pokemon is KO'd, it's unable to battle for that stock. So, for example, if Giovanni was trying to recover and had his Machamp sacrifice itself by throwing him back onstage with an Up Special, he wouldn't be able to call in Machamp until Giovanni respawned.
As far as an actual moveset, you could pull from all the weird anime shit like jetpacks and grabby claws, or go the other way and take the grittier elements from RBY and use whips, stun batons, brass knuckles, etc.
If we're going the duality / rivalry route, he'd also be a great rival to Mewtwo.