I do agree with (I want to say
MasterOfKnees
was the one who mentioned it) that making a Digimon and having their transformations as a well implemented mechanic would probably be a huge hassle to implement properly. And due to that difficulty, that'd be in and of itself something to consider.
And, like others have said, Banjo and Kazooie got a ton of support to be added to the game, while Agumon never really had that going for him, even now he's kind of niche. Or at least appears niche since there's no significant internet following for him in Smash compared to someone like Sora or even Dante.