If I had to make a Nintendo-only Fighters Pass, this is what I'd go with. I'm assuming that assist trophies aren't options (since they play an active role in gameplay), but spirits are options. (because it seems weird to rule out over a thousand characters because there's a single PNG file of them in the game)
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Min-Min (ARMS) - I'm not overly familiar with ARMS, but by my understanding, Min-Min's the most popular character. Plus, she seems to know kung fu, which will allow for some variety and make it so not all of her attacks have ludicrous range
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Elma (Xenoblade Chronicles X) - not sure if Rex would still be considered too late to make it into this pass or not, but we could use a Xenoblade character, and Elma's generally been used to represent XCX. Plus, I wouldn't want the game to be forgotten just because it was on the Wii U.
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Wonder Red (The Wonderful 101) - as far as I know, Nintendo still owns the property, and Platinum characters have already transitioned quite easily into Smash's style of gameplay. Plus, as the recent Kickstarter shows, the Wonderful 101 is still a decently popular property.
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Dixie Kong (Donkey Kong Country) - this seems like a no-brainer, and I find it weird that she hasn't been added to Smash yet.
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Bandanna Waddle Dee (Kirby) - it seems weird that Kirby hasn't gotten a new character since Brawl, and Bandanna Waddle Dee has been one of the core cast members since the Wii. Plus, given how much Smash's gameplay is based on the Kirby games, most of his moveset is already made, and he seems to be a popular pick even if some people dismiss him as a "Goomba with a hat". (which would be like calling Ridley a Charizard clone)
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Impa (the Legend of Zelda) - Zelda is long overdue for a new, unique character, but it seems like the best options are assist trophies. (Tingle could work, but it seems like he'd be a divisive choice) Ideally, they'd go with her Hyrule Warriors appearance, but if that's not an option for whatever reason (I doubt it, but Geno's a Mario character who's owned by Square-Enix, so I have no idea how this all works with Koei Tecmo), then her Skyward Sword design could work.
I would have liked to include more new franchises (Sin & Punishment, Eternal Darkness, or Custom Robo, for example), but I felt like some of the returning franchises could really use another character.