I'm not referring to the different health bars and comeback factor that comes with them, I'm just saying that you do have to think ahead while managing health and a strategy if you want to get the entire usage of these characters. I understand that Smash is tied to one health/precentage bar.
What I'm trying to get at here is that PT is similar to a team in team fighter games.
Using only one character you're skilled at with a set team composition, while being lack luster with the other one or two, will result in the opponent's favor unless you can contest and overcome them with the character you are soley good at.
While, yes, being skilled at multiple fighters in something like MvC is the nature of the game.
I'd also argue that it's the same with PT, not Smash in general, you're not getting the full advantages by not knowing how to use the other Pokémon.
So, it still equates to Pokémon when it comes to the one playing Red/Green.
Doesn't matter if you're great with one overleveled Charizard, once that's shut out, knocked out, and can't do anything against the current Pokemon out, you're left with the "team" that's been sitting at the same levels they were when you caught them and you might lean on them or not. Levels in this case are lab time/experience and familiarity with the character.
Sure, the opponent is still going to be facing whatever is thrown out in front of them, at a disadvantage or not, that's definitely not going to change unless they switch between matches. I understand where you're coming from on that point.
However, the player playing PT is still going to be imposing limitations and hindrances on themselves if they relegate themselves to one character.
Like in your original example, if you're extremely skilled with Charizard and only him, but ZSS is comboing you and not allowing you to react. Switching to Squirtle isn't going to help you at all, given you're lackluster with the character. So Charizard is still going to be combo food for the ZSS player or switch out and receive a similar result with Squirtle with a little to no chance of winning.
Also like you just said:
-matchup advantages don't matter if you're not near his level, which is going to be much harder to do if you're juggling much more characters around.
Learning how to use PT and his general mechanic will definitely require more effort and time than using one or two other characters, but that's the appeal and the reward of using them as interchangeably and fluidly as one unit.
Therefore, it's better to learn how the other characters work as opposed to only focusing on one part of the moveset. And with that I think you have to think of all three Pokémon of
as one character. Just view them as
apart of his moveset
rather than individual characters tied to a Down-B.
That's where I feel that mentality will separate the great PT players from the ones who are
just a great Squirtle, Ivysaur, or Charizard main.