Okay sorry to bring this back up. I was away for a while but I can't just let this slide. I'll go through each point one by one.
With Pokemon Trainer, all three characters are tied to each other. If Charizard dies, that mean Squirtle will have one less stock. But at the end of the day, it is still the Pokemon that are the playable characters and it is why Pokemon Trainer has three numbers instead of one.
Pokemon Trainer is still the key factor among them regardless. This is why you have to go through Classic Mode 3 times to get each trophy. Only Pokemon Trainer will always get a trophy, but you'll get one per Pokemon based upon your final character when you beat Master Hand(and sometimes Crazy Hand). It's still clear who the focus overall is. Pokemon Trainer is the actual main character here. The other 3 are literally the moveset. That's the mechanic in the first place. It works just like the actual Pokemon games. It's the Pokemon that does the moves, but the Trainer that properly controls them.
But you don't control the Pikmin. You fling them at your enemies and smack people with them. They are more like tools than anything. The only one you directly control is Olimar.
The moveset is entirely focused around what the Pikmin are, though. That's the reason it exists. Solimar is not a "normal" thing and simply possible due to the fact that the moveset's mechanics allow it, as it matches with the regular game.
Even in his own game the story focuses around Olimar or Alph and his team. Not the Pikmin. The first game opens up on Olimar and the objective revolves around Olimar. If the Pikmin were the stars, the game would be told from their perspective as this weird spaceman guy lands on their planet.
Yet the game is called Pikmin. Saying they aren't the main stars is a little silly. Olimar is the main protagonist. They're Co-Stars. Not unlike the Smash moveset itself.
You act like all Olimar does in Smash is stand around and summon Pikmin while the player attacks people as the Pikmin. No! You control Olimar, and you jump, dodge, shield and attack as Olimar. You are Olimar! You're Pikmin are your weapons. And you can even attack without them.
And as of Smash 4, it's impossible to play without the Pikmin thanks to the Up B. They're still the focus and the actual mechanic of the moveset. Olimar would not even exist as a playable character without the Pikmin being the focus of how it works. The point is you're supposed to use the Pikmin to fight, not jab attacks without him. That's the intended method. Again, due to how the moveset works, Solimar became possible. It's a consequence of the moveset mechanic(a Captain commanding the important Pikmin to fight), not some focus. And Solimar was removed, again, as of Smash 4. You also are attacking just as much with the Pikmin as you were with Olimar. To pretend they're not the focus of the moveset despite being the clear point of the moveset in itself(never mind being integral to the mechanic alone) is just looking at it... in the way it was clearly not intended. Also, for the record, you can't do all of Olimar's moveset without the Pikmin. Many Smash Attacks, aerials, and even his Up B are impossible without them(in two different ways in Smash. You can't do his Up B in Brawl without them because there's no Pikmin to use as a Tether. In 4, you can't do it without them because Up B is a Winged Pikmin). Also, considering the fact that his special moves directly revolve around the Pikmin, well...
Besides that, they aren't tools anyway. They're living beings and they emphasize this in Smash alone. To drive it home further, all of Olimar's renders include the Pikmin. As in his Smash renders. You know, the character portrait, etc? Even the amiibo have the Pikmin in. Even moreso, Pikmin have their own amiibo, yet Olimar clearly does not have a unique one without the Pikmin. It's so blatant they're a key part of the moveset that it's useless to deny this fact.
https://www.smashbros.com/wii/en_us/characters/pikmin.html In fact, this is his character page. Or should I say, their character page. In fact, the character in Brawl is called "Pikmin & Olimar". This is a Smash 4 oddity that he's somehow not key to the Pikmin, and it's a translation thing only. It's very clear the Pikmin are key to it.
The Legend of Zelda has "Zelda" in the title therefor Link is not the main character.
Zelda co-stars with Link anyway. As does Ganon. They're all main characters. There can be more than one. Being the playable character isn't the same thing as being the main character itself, which is the focus of the story. In this case, the focus is clearly on Link, but still also on Zelda and Ganon. In fact, the main characters are almost always variations of Link, Zelda, and Ganondorf, or characters that have similarities to their roles(I.E. Vaati and Marin. Or Skull Kid. Etc.)
Who care about how things work in their home games? Smash certainly doesn't. Dr. Mario is literally Mario in a doctors outfit. In Melee he heavier and slower but more powerful than Mario. Is there an home game reason for it? When you play Dr. Mario on the NES does it explain that Dr. Mario is in fact stronger thanregular Mario? No of course not. He was just an easy addition for the sake of an easy addition. And these echos are easy additions for the sake of padding out the roster. Nothing more nothing less. I can't believe you think home game accuracy matters in Smash. SMASH of all games! They could just make Alph a lighter and faster Olimar and people would just accept it just like they accepted Dr. Mario being a slower stronger Mario for no good reason.
Except the part where Dr. Mario was a last second clone and the only key difference was something unique to him, Megavitamins. In addition, he also unique music to add and was very very easy to implement. Besides that, unlike Olimar, Dr. Mario was focused far more on the Doc itself than simply the Megavitamins(his only unique point). The Viruses are the Co-Stars in it, but also don't show up beyond small cameos. Which makes sense, cause he's a clone. And the fact Pikmin & Olimar are based upon how they play in the home games. So yes, it does matter.
I'll once again point out Dr. Mario but also mention Dark Pit who plays exactly like Pit in his games. Finally I'll bring up how all the Koopalings are costumes even though it makes no sense for them to be. Seriously, I'm sorry, but your arguments are really bad given the nature of the Smash series.
Dark Pit has unique abilities as an option(Alph didn't), including the Dark Pit staff, and the inability to use the Three Sacred Treasures, the main reason he was cited by Sakurai himself to actually be separated. Because he couldn't do that move. Alph can do everything Olimar can do without any issues(I do agree using the same ship is silly, though). The only real difference is what the Pikmin, who again, are canonically a huge focus of the game(to deny this is ridiculous) itself as well as Olimar's story, can do. Now that the Pikmin have to be used in Smash no matter what(which is logical, since that was the point of the moveset in the first place), the only real way to separate the two is to have new Pikmin to focus on. This is the most logical way to do it because it'll bring something to the table. Besides that, it's clear Sakurai is trying to not add a huge amount of newcomers. Even with Echoes, at least the characters are severely popular and easy to do, but also are notable enough on their own merits and have some points to consider. Daisy got in because she, like Waluigi were severely popular picks, but also because she was easy to make. Daisy also is the 100% focus of her character. She doesn't co-star with specific characters as a focus of her own game(of which at best, that's literally one game, which she Co-Stars with Mario... who is already playable). Overall, other Echoes aren't just different characters with potential different abilities, they were also easy to make at the same time while bringing something different to some degree. Dark Pit has a new Final Smash. Daisy has new aesthetics. Lucina has no tipper, which while it doesn't change much, does make a difference. What does Alph have that really separates him from every other Captain in the first place? What key and unique ability does he have even in his home series that should justify it? Beyond the Pikmin, who again, and always have and will be, the focus of the moveset, he's got nada. No reason to do so. Literally one Pikmin exists and it requires a lot to make it feel unique(because it's not a simple model change but actually a fairly different model) but still work. At this point, if they really wanted the Rock Pikmin in, it could've just been an alt for the Purple Pikmin alone, but only under Alph's costumes. Of course, that's harder to implement, hence they don't exist in the moveset. So they kept him an alt because he's identical to Olimar entirely in his own game(bar having a slightly different size, but the proportions are the same)... just like the other Captains. This is the same reason why Pokemon Trainer has alts that not just reference other Trainers(besides that, PT does not have a specific name, being intentionally generic), but also now a female alt. He's a bit different from Olimar/Alph in that he's not directly playable, but still is key to the moveset's overall mechanic(Pokemon Change being the key mechanic, of course). Pikmin and the Captain are both key parts of the moveset. It's just that the Pikmin overall get the bigger focus due to how the moveset was designed. Besides the fact they always shared the actual slot name(FYI, it's still Pikmin & Olimar on the Smash 4 Japanese and Smash Ultimate Japanese website. There's a reason for that). Speaking of that...
https://www.smashbros.com/wiiu-3ds/us/characters/pikmin.html Look at the url name for even the US website. It's kind of obvious how important they are. Sakurai makes it verrrrrry clear. It's only Smash Ultimate's that ignores these key urls and just says a number, but that's due to the new organizational design. Nothing else.
The Koopalings are costumes because it would be impossible to make 8 unique movesets in that given time. The actual moveset is the Koopa Clown Car itself. The Koopalings work fine as costumes simply because they all have shared the exact same role as Bowser Jr., being Bowser's children and pretty much were bosses for Mario and Co. to battle. In fact, the only reason they are alts is because they were easy to make work due to the Koopa Clown Car being the moveset, so throwing them in took little work. It's in fact the same way Pikmin & Captain(which is a pretty accurate name) are done. Besides that, the alts are more or less deemed unimportant and just treated as extras anyway. That's why very few of them got amiibo.