Ok I have some time before I do some RTC stuff tonight, let me post this little shabang for series to make this easy.
Mario: It's perfect as is right now. Bowser, Bowser Jr, and the Koopalings rep it well. You could make a bit of a stretch and say maybe that Fawful could work but let's be real Bowser and Bowser Jr rep this well. There are no other real recurring significant antagonists other than Waluigi in the spinoffs, and we all know his sitch. Also Mario has so many good candidates for bosses, the most likely are King Boo and Petey Piranha
DK: Getting K Rool is great, as it means we have the main man for DKC. It is fine.
Yoshi: Kamek would be the choice but I can see why he got passed over and is on Mushroom Kingdom U again. He is not super popular, and the Yoshi games, while having him as the main antagonist, usually end up with Bowser as the final boss in some way shape or form.
Wario: Well Wario himself somewhat counts. But for real until we get that sick Wario Land reboot with Captain Syrup coming back, we are pretty much in this spot.
Zelda: Part of the issue with the Zelda series is outside of Ganondorf (and well, Ganon), there are no recurring villains outside of Vaati who has been forgotten by Nintendo. I feel if we get one, we will get Skull Kid due to circumstantial evidence and the fact that he is the most popular one off Zelda villain. Zelda has so many bosses I could go on for that.
Metroid: We got Ridley and Dark Samus. That's perfect.
Kirby: Meta Knight and King Dedede both are rivals/antagonists, even if in Modern Kirby they may not always be antagonistic. I guess Marx or Magalor could work but I highly doubt it. Also I am calling a Dyna Blade boss for story mode.
Star Fox: Getting Wolf back is perfect as the only other villain would be Andross who is awkward to work.
Pokemon: Mewtwo for all intensive purposes in Smash is a villain. He is the final boss of Red/Blue, looks to be shaping up to be the final boss of lets go, was the main antagonist of the first movie, it looks like they are remaking the first movie as the next movie, he fits the role. In terms of other choices, the pickings are harder. An Ultra Beast could be considered an antagonist, but only Nihilego and Buzzwole seem likely for smash. Mimikyu and Meowth could both be considered in the future because they are iconic, pushed in the anime (Meowth to a far greater degree), and have potential to be unique. Shame they are pokeballs. One thing of note is that due to many huge antagonistic legendary pokemon, they could make good bosses. Rayquaza (even if it is only territorial) could return as a boss, or you could do something new like Hoopa Unbound or Necrozma.
Earthbound/Mother: You have two viable options. Sorry Giegue. They are Masked Man and Porky. Porky has the benefit of being in both Mother 3 and Earthbound, being iconic, and would be unique. Masked Man could work as a Lucas echo with a separate Up B. Either way, both are not likely due to Mother being dead rn. If I had to bet I would go with Masked Man since as an echo his workload would be less but I could see both. Neither is null.
F Zero: I can easily see a Black Shadow echo for Falcon or Ganon. Falcon since same series, Ganon since he could pick up older Dorf moves. He has a fanbase, especially since if he got in Norio Wakamoto would voice him.
Fire Emblem: The Black Knight is in my opinion one of the most likely echo fighters right now. The mii costume, disappearing from the Castle Siege background, his popularity, it all makes him seem very likely to me. Also I could see a Grima Robin alt or a Grima boss.
Metal Gear: At best a Big Boss echo, but that is not likely. A Metal Gear REX boss fight could happen.
Sonic: Shadow as an echo seems super likely. Eggman as a story mode boss I also would buy.
Kid Icarus: Medusa as a Palutena echo makes sense, she could take up the moves that Palutena will no longer have in her customs. Hades could also work as a boss and hopefully will jump into codecs. Viridi is going to be stuck in codecs and RBF.
Xenoblade: There are some candidates for echos, but the best candidate comes from XB2 and I feel rn that it would happen with DLC rather than base game.
Final Fantasy: Sephiroth is a huge antagonist, but I do feel if we got him we would have gotten One Winged Angel, which as of now seems highly unlikely.
Street Fighter: I would love an Akuma echo of Ryu, but it seems that Ken would be chosen instead. I doubt we would get a SF newcomer.
Splatoon: We got Octolings... I guess?
Newcomers: Well Heihatchi is a bad man so if he is the Namco rep hes a villain. Same with Nightmare but less bad man and more Eldritch abomination. Felix as an Isaac echo could be one if you really push the bounds for a villain.
Everything else does not seem likely or relevant to me.