With Fire Emblem, I am mostly fine with the amount of representation that it has; however, I don't consider Fire Emblem's roster to be complete without Lyn. Lyn should be there. I also find Chrom to be pretty unnecessary. You could also cut Corrin without too much trouble if you wanted, I guess. But otherwise it's not too bad. They should've been more clear on Lucina being a lower-effort character when they revealed her in 4 (potentially leaving her out of the CG trailer), and they could've postponed both Roy and/or Corrin to Ultimate instead of making them DLC in 4. I think there would've been less complaint if it was done like this.
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Pokémon has some extraneous stuff. Representing Pokémon well is really hard because it has a lot of iconic mons. A boatload of mons are iconic, but that doesn't necessarily mean that every one should be in the game because that would really be overboard. So just pick a few of the most iconic ones and make sure you get a decent distribution of historical eras and typings.
Pikachu/Charizard/Mewtwo/Lucario/Greninja/Hoenn rep seems pretty good to me. You could drop Greninja or the Hoenn rep if you wanted, and/or you could add Jigglypuff back if you want the OG 12 preserved. You get an actually pretty great type distribution here along with something from the GBA, DS, and 3DS eras. I'm okay with Gen 1 getting a bit more because it's through the roof in iconicness, but I wouldn't want it to go too far overboard.
But whether or not you agree with the particular characters I listed there, the bigger point was that you can achieve a really solid and sufficiently diverse representation for Pokémon as a series (in terms of unique typings/movesets and representing series history) with around 6 or so characters.
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As an aside, without "Everyone is Here" we probably would've gotten something like Pikachu/Charizard/Mewtwo/Jigglypuff/Lucario/Greninja/Incineroar. This is actually pretty close to what I listed, just with Jigglypuff's grandfather clause and the loss of a GBA rep in exchange for the hideous fire cat.
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On Kid Icarus, I agree that a third rep is hard to justify. It's not really any bigger than other first party series that are unrepresented, like Golden Sun, Advance Wars, and Rhythm Heaven.