I think you're ignoring that Pokemon is a multimedia franchise, not just a gaming franchise. Combine the anime and cartoons, the movies, the trading card games, the toys, everything, and it towers over Mario a ton. Pokemon Go is considered the most financially successful Pokemon game of all time and that isn't even something that can be measured by sales.
See, I do agree with you to an extent that there isn't much difference between Mario and Pokemon getting a ****-ton of content than with FE and hypothetically Xenoblade - hell, I could maybe argue there's merit to the notion that putting Pikachu in Smash served a promotional purpose to Pokemon, at least in localisation (even if, again, small fries compared to mass merchandising; a Billboard 200 album; and being sandwiched between Batman and Animaniacs on the WB) - however, I think FE's treatment is a contradiction to the rest of Smash's roster-building mentality, where iconic factor of both series and individual characters is weighed very heavily when considering what to give new content - fans aren't inherently at fault for taking issue with that contradiction, especially when FE's modern Western existence is irreversibly and unfortunately (necessary-evil as it is) tied to Smash - either take down the exception or take down the rule, if the likes of Star Fox, Pikmin, Wario, EarthBound and Kid Icarus had 8 characters each, external contexts be damned, would anyone complain about FE rep?
I still don't get the complaints.
Marth was already a hugely popular requested pick for Melee. A fan favorite. And Fire Emblem clearly had a lot of popularity on the SNES with 3 games being released. Marth was even considered for 64.
Roy got in as a promotional pick, and a straight up clone. Their popularity resulted in the first localisation of the series, in fact it was planned for Roy's game to debut in the West but it got skipped in favor of the next installment.
Yes Pokemon got mass promotion and no indeed, it extended far beyond games. You named Pokemon Go but Fire Emblem Heroes did better than even Super Mario Run. It does great as a mobile game. Fire Emblem also had a anime show back in the day. Only had 2 episodes or so, but yeah, technically also a "multimedia" franchise. Even if significantly smaller than Pokemon (then again, what isn't?).
I really see no problem with it in the end. Cause its a simple cause and effect.
1: Fire Emblem did great in Japan, Fire Emblem got into Melee therefore by popular request. Characters are considered for removal in Western releases but kept in the end, and eventually warmly embraced by the fans.
2: Fire Emblem reaches Western audiences. It is nicely received. This naturally led to more Fire Emblem requests. Ike got into Brawl as a result.
3: Fire Emblem sales drop and Awakening revived the franchise and gave it a much needed boost. Awakening characters become highly discussed for this next Smash. We end up with 2 newcomers in Smash 4 and 2 through DLC. People become upset despite the characters involved have good reason to be included.
4: Three Houses releases, Smash Ultimste comes out. We only got Chrom as Echo Fighter whilst the rest returns and Byleth is a DLC character because of the great success of Three Houses. Everyone loses their mind.
Really counting out Echoes and Roy as a semi clone, there are just 5 unique Fire Emblem characters. Two full echoes who are quite the popular requests even, and for pure Echoes quite unique from their counterparts due to how their blades work.
Fire Emblem has a rotating cast too and very rarely are characters seen in future games unless by remake or sequels. So the fact we got quite a few newcomers after the massive success since Melee isn't even all that weird to me honestly.