There's actually a very large difference between the two's roles.
Waluigi was created to be #2's #3, along with the other things I explained in the post you quoted.
Isabelle, however isn't necessarily that. She is a secretary. Although it is true that she assists the player, she also guides the player in some cases. She has a goal of her own that doesn't revolve around others 24/7, which is to make the town a better place to live in. She's a workaholic, hard on herself, and even ignores her own physical health in some cases because of her love for her job. That would be a hard working secretary. Her boost in popularity since her first appearance as well as getting into Smash could potentially be a way of symbolizing just how much her hard work seems to have paid off. Isabelle wasn't necessarily created to eternally be in a sidekick's shadow, only daring to do whatever they did but better. She was created to not only act as an assistant, but a teacher in many ways; Isabelle has shown to be her own person, one that hasn't only become valuable to the player but the entire town of the player.