You could make the argument that Samus and Dark Samus have vastly different canonical skill sets that would stop them from ever being echoes, but that didn't stop Dark Samus from being added as an echo. If anything, Dark Samus taking on Samus' traits is much more of a departure from Metroid's canon than Tetra taking on Toon Link's moveset because Dark Samus has canonically been depicted fighting with a different style than what is used in Smash while Tetra is more or less a blank slate.
They have extremely similar animations and all of Dark Samus' skills are specifically meant to be better takes on Samus'. She's also using Samus' old armor, and thus, is capable of the same things. She's a very poor example. And also is disliked for not being unique. What exactly can Tetra legitimately do beyond a partial stabbing motion(cause Rapier) that's similar to Toon Link's skills? Remember, mods mean nothing. Her own skills got a showing, spin-off or not. Dark Samus doesn't take a major departure from Metroid's canon in Smash either way. She's basically just Samus, but upgraded, in terms of Metroid. The worst that happens is a lack of making her more unique in Smash. However, either way, she isn't a leap from her canon abilities. Just twisted a bit so it's kind of meh.
Additionally, I think the criticism that Tetra doesn't actually do anything (outside of Hyrule Warriors) that could be used in a Smash moveset applies to just about every Zelda character out there. Zelda hadn't fought outside of firing light arrows at Ganon in Ocarina of Time, but that didn't stop her from joining Melee. Likewise, Sheik just teleports, jobs to a shadow, and teaches Link various songs on her harp, but she also got into Melee. Other than riding a horse in Ocarina and blocking a couple of blows from/jobbing to Ghirahim in Skyward Sword, Impa is a walking exposition dump. Skull Kid steals a horse, turns Link into a Deku scrub, and makes the moon crash into the earth, with Majora being the actual entity fought. However, these beforementioned characters were/are all seen as viable Smash characters because they all have backstories that would give them some combat ability and only Link and the bad guys do much on-screen fighting in Zelda. I don't really see how Tetra is a departure from this. She's a pirate captain with a rough-and-tumble, no-nonsense personality that carries a sheathed knife on her hip. It's not a massive break in her character to imagine her fighting with a sword and shield, especially in a world where that's the norm.
We wouldn't have gotten Sheik without Zelda(or vice versa), and Sheik doesn't really fight either onscreen by that point. Yes, they were made up. Difference is they weren't Echoes in any way. Young Link fights corely like Link because... they're both Link. Ganondorf fights like Falcon because those abilities actually do have some relevance to him as well(besides just the tech demo). Ganondorf does eventually kick in canon, but also he created energy to do a ground punch, showing he still can punch. In addition, his Forward Air is literally fully changed to be a move from his own arsenal, via just artwork, though.
Impa doesn't matter because she's not playable in Smash in either. Almost all of these examples have nothing to do with actual playable Smash characters, or they came up only as ideas after certain characters came in.
To further clarify;
- Impa doesn't even fight till SS and HW in any possible way. She wasn't even a legitimate contender till Sheik, who pretended to be a Sheikah while under Impa's tutilage, was already in. And even then, she had no clamourings for till the idea of straight clones was more plausible.
- Also worth noting that she is physically capable even before this, sometimes in just various artwork. She's blatantly presented as super strong in the Oracle series, at least her official design is. The games don't go into much.
- Zelda does fight... by copying Link's moves, in two non-canon games, some comics, and a TV show. She clearly knows how to fight and is capable of doing so. It was never stated she's incapable of it. It doesn't matter if they're non-canon, because it means she can outright fight. In addition, we knew she was capable of some kind of magic, and then uses some magic in Smash based loosely upon the game her core design comes from. Where the only canonical moves she has is general telekinesis(she's able to open doors with her mind. Which, well... how hard can it be to grab a person in a similar way? That's not a stretch) and is transforming into Sheik.
- Sheik on the other hand is just imagined as a Ninja, which she acts and looks like one to begin with. She easily takes less work to think out, despite having more completely unique moves. It's also possibly just a case of Sakurai really liking Ninjas and didn't have to think hard on it(akin to Captain Falcon's inspiration from Japanese superheroes).
- Ganondorf is unique anyway in that he was lucky to get his spot. However, he wouldn't have if his abilities weren't at least somewhat close. Does he make a magical fist full of power and use a brunt force attack in canon? Yes. It's just obviously not the same kind of attack(it hits the ground, creating a shockwave. In Smash, he hits the enemy with a powerful brunt force attack instead). Gerudo Dragon is entirely random, same with Dark Dive. Wizard's Foot has a slight bit of animation from the earlier Ground Punch as he partially drop kicks down with a single foot during the animation, making it an aerial thing only. His Forward Aerial is being taken from official artwork.
- The other two Links are clones of Link in general and have nearly the same skills. They aren't a stretch.
...It really doesn't much apply to the Zelda roster. Every single clone(or echo, if one would come up) has some real basis on it. It's not just "they have the same bodyshape" alone. Again, what of Tetra's skills, and it doesn't matter where they were shown off, makes her remotely similar to Toon Link? In fact, exactly how many animations could she use to even be a semi-clone like, say, Isabelle is to Villager? They aren't the same bodyshape(which is why Isabelle can't be an Echo), but also can easily do the same thing(while they aren't the same exact skills) due to the series they're from having a lot of universal stuff. She's not perfect, as some items you never would see her use, but it's not hard to believe she could use a Fishing Rod anyway.
In terms of the Mario row, I don't really love it either, but I can't really think of a better way to arrange it. I initially tried putting Yoshi and Wario at the back and moving Dr. Mario up with the other Mario protagonists, but I really didn't like how Dr. Mario was wedged between a bunch of Mario mainstays, how Yoshi was behind Piranha Plant, or how Waluigi came before Wario and was separated from him by two characters. From there, I tried moving Dr. Mario to the first spot in the roster to match Melee, moved Yoshi to Dr. Mario's old spot to keep him with Mario's other protagonists while keeping the princesses together, and moved Wario in front of Waluigi. However, I really didn't like that Mario wasn't the first spot in the roster, so I moved Dr. Mario to the end with Piranha Plant as the two more obscure Mario reps.
...It's easy. Echoes are next to their normal person. Dr. Mario obviously is after Bowser, Peach, and Daisy,, since he was a last minute clone. In fact, let me quickly put the order;
- Mario
- Luigi
- Peach/Daisy or Bowser
- Bowser or Peach/Daisy
- Dr. Mario
- Bowser Jr. or Rosalina
- Rosalina or Bowser Jr.
- Piranha Plant
- Waluigi
- Yoshi or Wario
- Wario or Yoshi(I forget who appears legitimately first)
You can also put Yoshi right after Dr. Mario too, if you prefer Yoshi to be basically like he was in Smash For. Waluigi in this case would also be right before Wario, a more logical approach. You also have Sheik before Zelda, like their reveal order in Smash, but the reverse would probably make more sense with your roster being more based around, from what I can tell, game debut in their own series(with a tiny caveat that Yoshi is treated closely to Super Mario instead of his own franchise. Which is probably nicer, cause him being before Wario is awkward. If only cause that means Waluigi can't even sit next to Wario, his own partner).
Then this row fits what you want, accuracy. As Waluigi has no ties to WarioWare, he makes no sense in that placement. And since you're not doing Ultimate's "order of reveal", that leaves one other way. I'm not saying your way is bad, but I'm not sure if you were trying to be more coherent in terms of order. I agree Mario should be first too.
However, to further clarify the issues; Dr. Mario is a protagonist of his series. Why shouldn't he be wedged in with the rest? There's nothing unique about him over the others or vice versa. PP makes sense at the end along with Waluigi because both are characters who are minor to begin with. Waluigi at most started or entered a few plots, but he is very unnotable in stories. PP has no importance to any plot either way, and is at best just there for the sake of "we need some obstacles". That's why being at the end works better.
I get what you're trying to do here. That "less important characters are at the end", but you're also trying to do that while splitting up a franchise three ways to accomplish that, making the placement completely strange and illogical. That's the reason why Smash has tried to be fairly coherent with the idea. Clones were next to their counterpartin Melee, Brawl was pretty easily logical and had no one in odd spots. For(Four/4) did it a little oddly, but the last minute clones were in a special spot on its own. Ultimate 100% goes by reveal order. As Dr. Mario isn't here as some last-minute clone, he doesn't make sense near the end. The most awkward spot at best is how Echoes work, but the rest are very coherent either way.