By the way, you actually played AS the pokemon in the game, so that's why they chose Pokemon instead of the trainer for Smash Bros in the first place. Just after years of consideration by the team, Pokemon Trainer became a character... but you STILL play as the pokemon.
Be that as it may, the Pokemon Trainer was still the lead of the game and was actually playable to an extent (exploration, interaction, and Pokeball usage). Without a Pokemon Trainer, you can't be a Pokemon Master (selling point of the game & point of the game).
Basically, every pokemon has an equal amount of being added, mainly because each pokemon is not truly a main character with no true relevance of the game. You CREATE their relevance to the game. And only popularity will tell whether they'll be added to Smash. (Well, Mewtwo technically has relevance...)
The pokemon are not main characters and have no true relevance to the game (and still don't no matter how much you use and level them up), but Pokemon Trainer and Gym Leaders Mysty & Brock, the Elite Four, and Gary (Pokemon Trainer's rival in Blue/Red) are main characters and they do have relevance. You don't create a pokemon's relevance to the game, because no matter how much you level up Pikachu, he will never challenge a gym leader to a battle nor will he explore the Pokemon world and catch all 500+ pokemon for you. The pokemon are just instruments that the pokemon trainers use to heighten their standing in the competitive pokemon battling scene.
In the end, there was every reason to include Pokemon Trainer seeing how the trainer is undeniably a huge symbol of what the Pokemon universe is all about and as such is the reason why Pokemon games are structured the way they are.
But in Final Fantasy's case, the characters actually HAVE relevance to the story and game. Which is WHY Mog wouldn't be chosen. He NEVER has ANY relevance to the game. (Not counting that mini-fight when they aided you.)
Pokemon Trainer actually HAS relevance to the story and the game. You know this, but brush it aside just because he is only playable to an extent.
That fact is why, for example, is why a supporting character wouldn't be chosen over a main character.
You came away from your argument saying that the pokemon are not main characters with created relevance only to come back and say supporting characters won't be chosen over main ones? The pokemon ARE supporting characters and whether you like it or not, Pokemon trainer was and still is the captain of the ship.