each pokemon should be rated separately as they are completely different characters in their own rights, and the pokemon trainer rated as a whole as well. perhaps each poke in italics?
i'd say pokemon trainer should be rated as a combination of the best two of his pokemon. why? because a smart trainer will be able to use his worst pokemon wisely at the end of a stock (particularly if it is stock tank Charizard). or even better, knocking the opponent away at the end of their stock, switching to the least effective pokemon, getting a quick ko, then switching on to the second of your better pokes. so it isn't weighing pt down as much as a simple average of the three pokemon would suggest. not to mention all three have their own match ups where they excel.
say one of the pokemon was sonic. sure, he isn't that great. but he DOES have advantageous match ups. so you use him the majority of the time against that match up. but against other characters where he isn't as useful, you can minimize the amount you use him by smart, careful switching.
and none of the three pokemon are as bad as sonic is. :\ all three are at least mid (yes, even charizard). most accept squirtle and ivysaur as top mid or even high, but zard seems to languish on in a lot of bottom tiers. well i don't understand why, since he has excellent horizontal recovery, decent vertical recovery, quick, ranged attacks (specifically ftilt and dtilt) which lend to a good ground game, flamethrower, rock smash ****, very strong smashes, and a nice air game that lends itself to excellent gimping with his extra third jump. fair is nice, uair has a surprising hitbox and stays out for quite a while, dair is a serviceable meteor that needs timing, nair is decent for approaches, and bair is a two hit attack that when sweetspotted gives good knockback. he also has an amazing grab game with that long neck of his. and his surprising dash speed complements it very well.
sure he's big and easily juggled. but so are a few characters that are hanging out waaaaaay higher than zard is right now.
plus you can always use his down special.
and OBVIOUSLY, to use pokemon trainer effectively, you have to learn how to use all three pokemon efficiently. as if all three were your main. because that's what you are asking as a pt main.
clearly, no one is at that point yet, and likely won't be for a while. but if/when someone gets there, watch out. because honestly, having three separate characters at your disposal is an advantage, not a disadvantage (assuming you are skilled with all three).