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Mario is basically Mr. Nintendo! He just has to be in the game. There could be quite a few Mario echoes as well.
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Luigi would be an alternate skin or echo, but it was tempting to make him his own character because of Luigi's Mansion.
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Pokemon is insanely popular. Just look at what happened with the first few weeks of Pokemon Go. I've never seen that many people walking around in my town for that many weeks ever in my life. It's clear people love Pokemon, and Pikachu is the mascot for Pokemon. Pikachu is a must have.
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While it makes sense to have Pichu or Raichu as an echo, I don't feel they are relevant or popular enough to be included at this time.
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Nintendo was hyping up BOTW during Wii U and for the launch of Switch, dedicated a year of E3 just to BOTW, and it all payed off because it's praised by just about everyone and it's crazy popular. Even if BOTW didn't have the massive success it did, Zelda has always been a very popular Nintendo title. Link has to be in the game. If size/proportions wasn't a problem then the other two links could be echoes.
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Splatoon was one of the most popular games on the Wii U, and it helped sell the Switch (and the Switch online service). It's just a popular, successful series and it totally deserves to be in Smash. Octolings could be an echo too.
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Animal Crossing is just another crazy popular game that Nintendo has. Also fits with Nintendo trying to be all cute and family friendly. Isabelle and probably some other characters could be alternate skins/echoes as well.
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Everytime I hear about the Xenoblade games I hear that it's the best game that the person has ever played and I hear about it a lot. It's clear it's popular. Personally, if I had all the time in the world, I'd probably be one of those people too. However, just watching Chugga Conroy's playthrough where he cut out ALL the grinding and repeats battles, it still took forever to watch through a playthrough of Xenoblade. I loved the game though from what I saw though. Xenoblade is bigger and better I would assume, and I bet it'll just keep getting better and more popular overtime. Shulk deserves a spot. I don't know Xenoblade well enough to know if Shulk could have echoes... I mean I could imagine Dunban being an interesting take because he would have some sort of mechanic that would severely limit his Monado usage, but make up for it in other ways. Perhaps Xenoblade 2 might have a character that could be an echo as well.
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I don't know much about Fire Emblem other than it's crazy popular. I hear Marth is the most recurring character so that's why he's here. I'm sure we are all familiar with how Marth can have many echo fighters. I personally want to get into the game because the perma-death mechanic interests me. I like it when games make you get attached to your characters.
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I honestly have no idea how popular Kirby is compared to other Nintendo titles nowadays. Though the Kirby games seem popular enough still, and also go for that family friendly vibe as well. Helps that he's pretty unique and the gameplay in the newer games is pretty smash-like nowadays which could get more casual players to transition into kirby games (and thus other nintendo games once they know nintendo makes multiple nice game series), or kirby fans to transition into smash easier.
As for unlockables
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Donkey Kong used to have a ton of great games, but nowadays you don't get a lot of DK games and the series doesn't seem as popular as it once was. Though they are still praised quite well, and some older gamers could appreciate seeing DK in the game. Also it's nice to have a heavy character. Perhaps Funky Kong could be an echo?
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Yoshi has a few games recently that have been advertised a decent amount compared to other remaining unrepresented series. Also another family friendly character that is unique and somewhat popular.
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The Wii was a crazy outstanding success and the Miis would be good to remind people about the Wii days. Also it's good to have custom characters. I was thinking about Wii Fit Trainer earlier, but ultimately decided against WFT because Miis cover a wider selection of games and allow for people to have fun with making their own characters to get in smash.
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Metroid has a very strong fan base, and it seems Nintendo knows this because they have the guts to be fine with just showing a logo of Metroid Prime 4 and that'd be it, and that was very effective. They seem to be giving Metroid a bit more love in the recent years compared to other series in the honorable mentions. Dark Samus or some hunters could be possible echoes. Of course, Metroid Prime 2 ECHOES makes it tempting to just leave Dark Samus as an echo.