Woah. Lots of replies since I was last on here. Let's see...
Toon Zelda is still Zelda, no? Besides, LoZ isn't the only franchise with a revolving cast that reuses characters. Anna from FE has made numerous appearances throughout the series.
As you said yourself, the only reason BotW's characters seem less important than the characters you listed is because the game didn't put a heavy emphasis on story. It's not fair if you're comparing characters from a game that doesn't focus on story to ones that come from a game that does. That's like saying that Marth is less important than Robin just because the latter debuted in a game with a deep story. You have to look at BotW itself. Compared to the other characters in BotW, the Champions had a very large role.
And it's not like the Champions immediately fell into obscurity. They got amiibo and their own DLC to keep them relevant. Did Groose have any of that?
Exactly. Believe me, I know Midna or Tingle are the more logical choices by far, but it feels like their time has passed. The library of Zelda games keeps on growing, and looking at Sakurai's most recent additions to the roster, relevancy seems to be a big factor in deciding characters (especially with Pokemon and FE).
Pretty hard to hate his enthusiasm.
https://www.gamefaqs.com/boards/632936-the-legend-of-zelda-breath-of-the-wild/75154927
This is the only one I could find. Urbosa seems to be the winner of this poll, but Mipha isn't far behind. At the very least, I think we can conclude that the female Champions are more popular than their male associates.
Unsurprisingly, Mipha wins the popularity contest in Japan by a landslide. Not sure where the other Champions stand though. I think it's worth looking into their popularity too before handing the hypothetical roster spot to Mipha.
I'll admit, Mipha's voice acting was abysmal, and Sidon easily stole the spotlight from his older sister. Still, she does have one advantage over the other Champions. The people who knew her are still alive, and you get to hear them recount their fond memories of how she effected them. I thought it helped a little to expand on her story. At least she was handled better than Revali, who, aside from his tsundere personality, had little to go off of until the DLC.