I posted my initial thoughts yesterday with my spirit dump but I'll expand on them a bit more here.
I just want to start off by recognizing that there are arguments for basically every third party's inclusion is smash, and most of them are valid. If Smash started as a crossover of companies instead of only focusing on nintendo, I wager most of these would have been in by know. With that out of the way, I'll blitz through some iconic faces which would probably be in if it weren't such a Nintendo centered game and there were unlimited slots. Rayman, Doom Guy, Master Chief, Sora, Agumon, Heihachi, Lloyd/Yuri, Jack Frost, Black Mage, Tails, Knuckles, Eggman, Shadow, Phoenix Wright, Conker, Battletoads, Ryu Hayabusa, Bomberman, Bill/Lance, Crono, Lara Croft, Slime, Layton, Jibanyan, Klonoa, Monster Hunter, and the list could really go on forever. Notable indies also include Shovel Knight, Shantae, Sans/Frisk, Cuphead, Quote, Reimu, Zagreus, and countless others. With that out of the way, I'll expand more on the first parties which I think are missing.
Dixie Kong - The third member of the DK crew may just be the most glaring omission, not only in our roster, but also Ultimate's. Although the Donkey Kong series is not as large as it used to be, overall the Donkey Kong Country series is one of nintendo's highest selling series. Additionally, unlike some of Nintendo's platformer series (sorry Kirby), the Donkey Kong Country games are also regarded as some of the best platformers of all time. Dixie's also a prominent female protagonist, which is always a plus. She was planned for Brawl, showing she was even considered by Sakurai. Finally, by the looks of things we'll be included Funky Kong as an echo at some point down the line, and personally I'd rather include Dixie before Funky.
Geno - While some will debate on whether or not he was the most important rpg character since sliced bread, or a completely irrelevant one time appearing spin off mario character, its undeniable that Geno is the largest request from the smash fanbase still not included in the thread. While the Geno community isn't as large right now as in previous times, its large support bases during Brawl and Ultimate DLC, as well as Legend spirit, Mii Costume, and recognition from Sakurai all make him an essential part of smash history. While I'm almost entirely neutral on his inclusion it would feel strange to have a discussion about most wanteds without mentioning Geno.
Zelda Rep - I don't think I need to explain myself too much here, but the Zelda series is long overdue for another rep. Nintendo's second biggest fully owned series hasn't gotten a new rep since Brawl, or even Melee if you consider Toon Link a spiritual successor to Young Link which I personally do. On top of that, all six of the current Zelda fighters are triforce users, which while I enjoy all of them, does feel like we're missing out on the rest of the Zelda cast. While I imagine we'll only be including one Zelda character if we do include one, personally I think the roster could handle two. My top picks for a Zelda newcomer would be Skull Kid or Midna & Wolf Link, but really any non triforce fighter (besides a champion because I can't see Nintendo choosing one over the other three) would fulfill the Zelda sized hole in the smash roster.
Chibi Robo - Hard to say much about the status of his series after zip lash (ew), but he does have an amiibo. Seems to be the next in line old IP to be included to smash fans, not completely sure why though, as that are lots of other IP's like Advance Wars to take a rep from. I personally Love Chibi Robo though so no complaints here.
Officer Howard - One of Nintendo's newest IP's which sold reasonably well for a new IP as I understand. Also lends themselves to a unique moveset with the Legions. We've also got some megafans in the thread so I think this is more a when and not an if for this project.
There were a lot of other characters I could have discussed, although I'm of the opinion that most first party characters at this point are icing on the cake, as opposed to truly missing from the roster. I do hope we include some of these later down the line in the project, although If this were a real smash game I would more than gladly take our current roster. Looking forward to future newcomer jobs!