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Geno - My most wanted, so that's pretty much a given for this one. He's just so different from every other possible candidate and such a big fan request. If not him, then Waluigi.
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Skull Kid or Midna w/ Wolf Link - These two have a lot of potential to be unique, and Zelda desperately needs representation outside of the triforce newcomers. I mean, is it alright if I add both considering just how long Zelda has gone without a newcomer despite being one of Nintendo's largest franchises???
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Sceptile - One of my favorite Pokemon of all time, and we need a fully evolved grass starter in my opinion. Plus Sceptile is just cool af.
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Sylux - Apparently he's going to become a bigger thing in the next game. He's got a cool design and he's not just a standard marine. Metroid is pretty well represented after this game though.
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Dixie Kong - She's one of the biggest missing pieces of the moniker Nintendo All-Stars and she could have such a good hair based move set.
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Marx - I support Bandanna Dee for the many fans he has, but if I'm adding a Kirby character I'm personally interested in, Marx is the best bet for how crazy he looks and how awesome of a move set he could really have.
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Lyn - Screw it, Fire Emblem is already so poorly represented, might as well add the character I want. I love Lyn like a lot of people for her being my introduction to the series. If you focused on her katana and bow properly, not giving her boring old sword moves, she'd work really well I think.
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Tom Nook - He deserved a spot this game, and he's probably the most recognizable face of Animal Crossing at this point across the entire series. Put him in.
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Krystal - She's much loved and fan requested. Plus she could have a really cool staff based move set, and I'm all for that. Plus, she's less of a joke character than I feel Slippy would have to be.
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Mii Mage - Because if you're going to keep focused on these Mii fighters like you are, not having a proper mage class selection is just a little dumb.
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Eh, just make Alph a proper Echo with Rock Pikmin, that'll do just fine.
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Medusa - She'd just look cool. I'm mostly against new Kid Icarus characters at this point, but if I have to pick, she's definitely my choice.
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Ashley would be a great mage with a now very popular fan base to represent Wario Ware. If we're talking Wario Land, Captain Syrup.
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Kamek just to add another OG villain and clearly after Piranha Plant he's much more reasonable. Let's add a Boshi costume for good measure.
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Elma - I like her design better than Rex I guess, and having dual gun blades with a lot of projectiles and maybe even incorporating a Skell would be really cool. I also just need to play more of Xenoblade Chronicles 2 before I make that decision.
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Retro Rep In General: Excitebiker or Mach Rider - Just something very out there with a bike being heavily featured in a move set is something I want to see realized in Smash.
Third Party Section:
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Chun-Li - Pretty much the undisputed second most recognizable character in Street Fighter and she'd just look really cool alongside him.
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Zero - He's just the coolest option for another Mega Man rep and has a lot of cool moves. His assist trophy status is a little heartbreaking.
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Alucard - Basically see Zero, but even more so as I love Alucard from Symphony of the Night and III.
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Raiden (As a Cyborg) - None of this Raiden mirroring Snake junk, I want the crazy look Raiden from Revengeance.
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Tails - He's the Luigi of the Sonic series, I just feel like he fits perfectly. Kunckles is also a very reasonable candidate for this position.
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Mrs. Pac-Man - She is all you can really do, and I think she'll probably just be an Echo.
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Rodin - Since Bayonetta already has Jeanne colors, I'd like to see Rodan have a unique move set with some of the weapons he forges from Inferno.
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Black Mage - Not going to lie, I don't know as much as I should about Final Fantasy and I don't really like many of the characters post VII anyway, nor am I super attracted to any characters before, so I'll just go with the basic choice.