That's a bad comparison. These are a set of recurring characters(never mind iconic ones). 4 characters who have kept the same artstyle since their debut, or all updated at once. Toon Link almost sticks out, if he didn't have a pure niche and wasn't basically just a clone(and wasn't the exact same kind of update, all 5 being brought to their unique GameCube designs, all of which also fit their moveset best. Toon Ganondorf is vastly different from TP Ganondorf, to say the least). Ganondorf is too important to be left out just literally for the sake of it. He's the franchise's key villain. He's important too(and also why they don't de-clone him as to keep previous players happy, making it easy to adjust to his changes).
The Pokemon all got updated to match their latest designs, but also kept certain Smash elements. Both Metroid characters got updated, not 1. Just adding a new character in a franchise doesn't mean much. When you update a franchise full of characters, consistency helps making them look more presentable. It also helps that their playstyles are adapted based upon the actual design. Toon Link is vastly different from Young Link despite both being the same kind of clone, due to things like the stubby legs, and has many different moves. Link did get an update, but it didn't change his core that much. Ganondorf actually plays more differently due to the extreme loss of speed, but still kept the focus on what he was, a brutal character.
It's not as simple as a complete aesthetic update. You have to make sure it still works well for their moveset. With no way to update Ganondorf(which means he sticks out even worse than Toon Link does), you just leave a really weird looking set of characters, who are blatantly tied to each other design-wise.
You can easily update or ignore Shulk when adding a new character. Nothing changes. If you update the Mario designs, you're left with some who have no way to be updated, so you need to make up some designs for their artstyle. So if they can put together a proper Ganondorf and Sheik BOTW style, that'd be great. Otherwise, TP all over again is honestly realistic.
Well, it's easier to post it in the Roster thread, but you already took care of that~
I will say I don't expect that large of cuts. But otherwise, seems solid. However, KI getting 3 seems a bit silly with Kirby having less than 2/3. Viridi is neat, but she shouldn't be in there while other franchises are super low. IMO, Kirby should have his core 3. I can get why you cut Falco, as he's not as important when you are making a tiny roster. That said, serious issues with your Zelda cast. Ganondorf absolutely needs to be in. Toon Zelda isn't that important in comparison, and even less important than Toon Link. Sheik is an understandable cut in this case, because Ganondorf absolutely should be there(or Ganon if needed). Likewise, Bowser needs to be there too. If you're going this low, Rosalina's a more understandable cut. The core cast should be there before the newer(albeit important in their own right) characters. Is Jigglypuff really necessary in this case? Why not put Lucario, Mewtwo, or Greninja there? I don't think Viridi or Toon Zelda has a big chance at this point. Uprising is already done, and there's no hint of a KI game coming that's new. Toon Zelda pretty much has only one workable gimmick, and Zelda already has that with her Phantom Armor move. Besides, Toon Link is vastly more important(as I said before) and has no business being cut.
Overall, I'd suggest making it bigger and adding the core cast back(and the original 12 being there, of course). Being Toon Link, Ganondorf, Bowser, Falco, King Dedede, Meta Knight, and there's little reason to cut both Capcom options(MegaMan is a bit more important, as he's a bigger icon than Ryu, although not by a severe amount). Pac-Man should stay. As for Pokemon, at least add back Lucario and Mewtwo/Greninja. They should have at least 3-4 characters even on a smaller roster. That said, if you don't return MegaMan or Pac-Man, Duck Hunt should be there for your 40th character.
...Wait, no Fire Emblem characters? Uh, no. It's too important. I can understand not many for obvious reasns, but Marth has to be there. Whether 2 is necessary is hard to say, but Ike or Robin would be good second choices for diversity/importance.