Yeah, way to ignore the franchise in question. Popularity's not the biggest factor for most franchises at all, true - except in the case of Pokemon.
Pikachu had done nothing for the original Pokemon Red/Blue. Jigglypuff, less so. But Smash 64 put them in because those were the Pokemon most popular at the time - and as we can see in Jigglypuff and Mewtwo's case, just because you're time's gone doesn't mean you don't get back in. (Sorry, Pichu.) Even today, Pikachu stands on a pillar built out of popular appeal, not out of the foundations of game design that elevated Mario, Link, and all the rest.
If you debase popularity as a Pokemon candidate's pillar, then you do it to all of them. Lucario and Greninja would be furry fads who would've been cut at the first opportunity. Mewtwo and Charizard would be a bunch of outdated fossils that had no reason to get in in the first place. Decidueye drops to the same level as his starter siblings, and Lycanroc loses all arguments and becomes yet another example of generation chaff - why add him over Kommo-o? Araquanid? Crabominable?
Popularity in general is fickle, yes. That's why we only see Pokemon as having good chances when their generation is the latest. Just take Zoroark - why did we espouse him when there were plenty of other Generation 5 Pokemon to choose from? Why did his chances die as soon as Generation 6 arrived? The same happened to Sceptile and Blaziken too - weren't they beloved by fans? Didn't they have the moveset potential and fit into Smash perfectly? How come no one argues for them anymore?
And this is all assuming that Mimikyu even loses its popularity, which isn't something anyone should be making bold claims about. I can say for certain, however, that everyone else in Generation 7 stands to lose a lot more than Mimikyu does once the generation shift happens, because only Mimikyu's based on an idea that exists outside of its own generation.
I don't like relying on popularity as an argument, and it's because
not even the Pokémon in Smash were chosen because of it. Pikachu was
prominent from the get go, featured in the anime, manga, and eventually became the face of the franchise. That prominence led to popularity and also led to being the face of Pokémon in Smash as well. Prominence at the right time has been a constant every time a new Smash game as come around. Take it from
Sakurai himself:
Well first of all, we talk with the Pokemon company. What’s the hot Pokemon? What Pokemon are in the movies right now? And really do a lot of research on that front.
For example, X and Y are coming out – of course, we haven’t done any market research because they’re not out yet, but we look at the animated series or movies and anything like that and again, find out which ones are going to be central to any of conversations in Pokemon going forward.
But it’s not just that – going back to just what we talked about, what’s unique about them? Where do they fit in with the rest of everything else? What do they have? It’s a combination of those things.
Notice the emphasis on asking who will be important going forward? They aren't asking who the fans approve of, because that skirts toward the risky and unpredictable.
Sakurai and his team look at prominence, not popularity, and I've been trying to point that out since Smash 4 speculation to little avail. Charizard, Lucario, Greninja, and the rest have not lost their prominence despite the spotlight moving on to other generations, and when combined with their unique abilities and the fact that their home franchise hasn't been on hiatus, explains exactly why they've stuck around. The only 'mons we've seen miss the cut have either been clones or were part of the logjam that is Gen 1 in Smash--Mewtwo was low enough priority to be a narrow miss in Brawl and in 4's base roster because the newer characters were deemed higher priority than the front-heavy number of older ones. Sakurai thinks the newer stars matter too!
This is why support for Zoroark, Sceptile, Blaziken, and the like has died down despite them being just as popular as ever: enough of their fans know that it's not their time right now. One needs to be prominent
and relevant to get into Smash, and they have the former but not the latter any more.
Popularity is not the determining factor here, even though it may seem that way at first. There is something more going on under the surface. Though it still only goes so far, since being a big enough deal only gets you far enough to be considered. From there, you need to be able to stand out.
Sheik and Squirtle didn't hurt Greninja's chances none. No one else has a body type similar to Mimikyu's, not even Pikachu, because Mimikyu's limbs come from his feet. Elemental uniqueness isn't a strong argument when Pokemon has about 12 more to feature, and Smash has no urgency to go down the list.
Greninja overlaps with Mimikyu more than Ganondorf and Mewtwo do, and that's just for having Shadow Sneak.
While Smash doesn't check off boxes for untapped elements or anything, having your entire set of abilities built around something no current character can come close to is pretty damn unique. Mimikyu may have a unique body type (one that may present some issues, mind you), but
both Decidueye and Lycanroc have unique builds of their own--ones with fewer potential issues--and movepools built around completely unique elements. Your mileage may vary, of course, but from the perspective of a designer making drafts of character concepts for them all and weighing their options, it seems like Mimikyu has less upside than its counterparts and more hangups that have to be worked around.
And for what it's worth, by the time Greninja was chosen, they'd probably already known Squirtle was far down on the priority list and wouldn't have much of a shot.
Sakurai made Villager work. Made R.O.B. work. Made Ivysaur work.
MImikyu is not going to be harder to make than those characters. T
He also couldn't make Chrom work, couldn't make the Ice Climbers work on the 3DS, and hasn't yet found a way to make Ridley work.
Just because Sakurai and crew have found angles for characters that we never considered before (Wii Fit Trainer fighting with yoga poses and exercise equipment!)
doesn't mean they are the MacGyvers of fighting games. We shouldn't count on them to figure out what we can't.
Personal pet peeve of mine. If you think your favorite could stand out in Smash, go ahead and make a character concept for them! Don't count on Sakurai to bail you out, show everyone what you see in them!