I don't see why the game needs more villians. The roster arguably only 'needs' to represent Nintendo as well as possible, and it just so happened that Ridley and K.Rool were some popular characters, and were both villians. They both deserve to be part of Smash, but not because of their status as villian, but because they're popular and important Nintendo characters.
Of course they have more history with Nintendo, on account of being older, but that doesn't mean that much. A character can be new and already be very major to Nintendo (Isabelle and Inkling for Ultimate, or Pikachu back in the Smash 64 days). Fact of the matter is that AC is a bigger deal to Nintendo than a lot of other series that already have 3 characters in (Star Fox, DKC), so it just really needed a second character, and Isabelle just so happens to be the most popular choice. So she deserves her spot just as much as Ridley and King K.Rool do.