Less unpopular and more underdiscussed, several of the representation-based issues that fans bring up most prominently can be pinned on Smash 4.
Most of these complaints didn't have much justification circa Brawl, or were even directly contradicted. Kirby had music from a sufficient variety of games created without Sakurai's direction. Sonic was able to emote properly. Fire Emblem was chugging along at a normal pace. Series like DK and Metroid would be demanded more content after the fact, but the addition of Diddy Kong and Zero Suit Samus were notable steps toward a better position - stages like Frigate Orpheon and (love it or hate it) Rumble Falls were pretty unique compared to what would become the stereotype for these series' more samey locales.
With Ultimate, we have to consider how limited the scope of new content could be in base game to begin with. Longstanding complaints about DK and Metroid subsided with new character additions. But common criticisms such as Kirby's stage representation, Fire Emblem bloat or Sonic being how he is were not high priority issues. Zelda got a lot of attention, but moreso tweaking the veterans who are already here and adding Young Link back over bringing in new blood. I don't think you can blame Ultimate for anything directly as much as you can just disagree with its priorities, and insistence by design to maintain tradition and status quo. Radical change was in contradiction to its core philosophy.
Perhaps by circumstance, but Smash 4 then becomes the black sheep of the series. I personally have little to no gripes with the roster selection in particular. Stages draw some ire, with some questionable choices for Kirby and more of the same from Metroid and DK... I'll defend Jungle Hijinx for its unique gimmick though. This is where some grow concerned about Zelda's roster stagnation, receiving no newcomer this game while Mario and Pokemon handily surpass it, and underdog Fire Emblem boosts ahead from behind. Sonic is left in an awkward place due to Sega's own brand mishandling, likely directing Nintendo to ease back on the attitude and create the bland Sonic we have today. This is famously the period of time where Sonic seemed perpetually embarrassed of itself.
I don't bring up all this stuff to criticize Smash 4's choices entirely though... just to point out that many of these passionate issues within the community are simply targeting the decisions made in one single game. Ultimate being a game celebrating and maintaining series history, with a restriction on how much new content could be added to base game, doesn't do much to alleviate these issues. But once the series returns to form and moves forward as it used to, I think we will find that many of these complaints aren't as dire as they appeared. Fire Emblem having eight characters, four of them with a similar moveset framework, is clearly a result of Everyone is Here and not much more... as is Zelda's current state, with most of that energy going toward revitalizing veterans. Most series did not receive a single stage, so it's hard to say confidently where a series like Kirby stands. And Sonic was in the tail end of this rut during Ultimate, with a very fruitful few years and a successful brand revitalization accomplished since.
TLDR, many of the assumptions the community places on Sakurai's decisions and questionable "representation" is circumstantial carryover from Smash 4, into Ultimate - a game that did not and could not evolve the character or stage roster very far prior to a third party dominated run of DLC.
