Second place to Skull Kid for me is Midna, but considering her fate is sealed I would choose Vaati. Link would have Ganondorf, Young Link would have Skull Kid, and Toon Link would have Vaati. It would be absolutely perfect. Vaati should ideally appear normally in his Minish form, but have parts of his body transform into the one-eyed tornado monster for attacks. It would honestly pretty sick and a perfect villain for the Hero of Winds.
I always felt that Midna would be best without a big animal attached to bog her down. That way she could move gracefully, teleport, disappear into the ground as a shadow, and all the other amazing stuff Midna does. Wolf Link is just a wolf that bites, scratches, tail whips, etc. Doesn't add anything to the package except looking badass. Pros of ditching the wolf outweigh the cons, despite my love for Wolf Link's design.
Out of the BotW champions, I'd easily choose Revali. He's the first Rito that can actually fight, was quite memorable, and could have a simpler moveset that's still pretty flashy. The Rito maintain popularity from WW and Revali was generally well recieved himself. Others hated him though, so I don't know. I envision him maybe borrowing from Falco for melee attacks and primarily using different arrow types. Perhaps he rotates elemental arrows with down-B, fires them with neutral-B, uses his signature gale move with up-B and has some kind of mobile side-B.
Of the Six Sages, Impa is an absolute no contest. Being the Sage of Shadow can give her really cool dark particle effects on attacks. Or, if they went with SS Impa, make it a light themed moveset instead. Or maybe use an almagate version of Impa where Sakurai invents whatever he wants for her (more likely). Or settle for an echo (the realistic outcome).
It would be cool to see a Goron or a Zora in SSB. Both are recurrent enough to be recognizeable and have lots of moveset potential. There are a few to choose from, but let's face it: Darunia and Ruto are the iconic ones. Other similar characters of said races that came in later Zelda games feel like throwbacks to the classic sages.
Of course, I will mention Fierce Deity Link. Not a character I even remotely expect, and I especially wouldn't want to make people suffer a 4th Link on their precious character select screen, but by jove mate. Wouldn't it just be freaking awesome? I mean come on, with the sick looking armor and the Double Helix sword, he would just be a dream come true. I guess you could work him out as a wild hybrid echo of Link and other heavy-sword users like Ike and Shulk, lol. It's a guilty dream.
And last, I'll always have a soft spot for Deku Link, as he is personally my favorite of the three mask forms prominently in MM.