To be honest, I've never quite gotten the appeal of transformation characters. Like, a transformation character is just, like, two movesets arbitrarily stapled together most of the time. Am I supposed to use both? Because that's probably not what's going to happen. It's certainly not what happened with Sheik. What am I supposed to do if I only like one? When am I supposed to be switching? I just have no idea how I'm supposed to feel about these sorts of characters.
This was originally written as one paragraph, but I decided to chop it up for readability.
They're not arbitrarily slapped together, they're done because of the ties the characters have to each other, and they're designed to compliment each other.
People didn't use both Zelda and Sheik because Zelda was a terrible character, and the technology couldn't really handle the mechanic all that well (transforming took too long). People didn't use Samus and Zero Suit Samus because they literally couldn't. It was more of an Easter egg than anything else, and wasn't really a part of their moveset.
The only liking one thing is the argument I think is the strongest; since transformation characters are multiple full characters, I don't think it would be too much to ask for the characters to be available alone as well. Though it could be argued that if you don't like all of the movesets then you don't like the character as a whole, as they are designed to work together. That is their point, and it's where the properly designed one shines.
On that last point though, I think a pretty simple solution to this problem for the Pokémon Trainer, is to allow players to choose their Pokémon. So, say all Pokémon return in the next game (they wouldn't, but say they do). Each Pokémon could be played alone, but they also had a secret "Echo Fighter" designed to work in conjunction with the other 10 Pokémon on the roster. If you wanted to play as the Pokémon Trainer, you would be able to pick any 3 of those 10 characters, granting you with a lot of previously unseen strategies.
For example, you could use Pichu, and then switch to Lucario, buffed by Pichu's self-damaging gimmick. Or you could use Squirtle to close in the gap before switching to Incineroar to force your opponent to deal with your ludicrous damage. You could use just about any Pokémon in conjunction with Jigglypuff to make your offstage play some of the best in the game. With how diverse these characters are, the possibilities are pretty endless.
EDIT: I should add that this isn't something that I would do for all transformation characters. For example, if we got Amingo, SonSon, & Ruby Heart as a transformation character, they would be inseparable, as their mechanics were meant to emulate Marvel Vs. Capcom's 3v3 style.