That is actually why I think it is unfitting.
Both Alph and Olimar have pretty immediate personalities in the game. They get little air time, and it is filled with humor.
I'm sure that if we had got Alph as an echo, that Sakurai would've given him some more unique animations for him to stand out more.
But as they are right now, the animations are simply very generic and basic as it's been pointed out.
And I guess that, considering their Japanese name being "Pikmin & Olimar/Alph", thus putting the focus on the Pikmin reminds me of Bowser Jr. and the Koopalings.
Bowser Jr.'s moveset is centered on the Clown Car more so on the innate abilities Bowser Jr. may have. Likewise, the animations he has for taunts and win poses are generic enough to work well with the Koopalings.
Taking this in consideration and how the focus of Olimar/Alph is the Pikmin, it seems to be a similar case. The focus of the character and the moveset is the Pikmin, but they need someone commanding them. Olimar and Alph, being the main protagonists of Pikmin 1/2 and Pikmin 3 respectively, fill that role since that's primarily what they do in the game.
A Red Pikmin is still a Red Pikmin regardless of who's throwing it, after all.
Sure, this leads to oddities such as the Koopalings transforming into Shadow Mario (although that's basically the power of the magic paintbrush rather than a Bowser Jr. specific thing) and Alph using Olimar's ship, but those are minor things.
Had Dark Pit not had the convenience of being able to borrow the mechanics of Zelda's Light Arrow for his Dark Pit Staff Final Smash, he probably could have remained a costume for Pit, but I guess we'll never know.