I legitimately forgot that. Though it doesn't change that Mother 2 rehashed Mother 1's story. Giegue and Giygas are extremely similar for a reason.
The problem is, he works as an Echo just as much. Already owned up to the correction on the Porky thing. My bad(it's part of this post a bit up above).
Here's the thing with the Mother Protagonists; they are designed so they represent the game's vast abilities moreso than themselves. That means that besides that Nintendo can work perfectly as an Echo(since he's an easy addition and outside of needing some design changes so you won't confuse him with Ness, which is pretty easy as Dark Pit shows), he also is important to show off the other things specific to Mother 1. The weapons, abilities, etc. Like instead of using the Bat, he could use the Katana that one of the other members has for his Smash attack. Stuff like that. If he's a carbon copy of Ness, which he perfectly wells fine as overall, what does he bring? Echo or not, the important part is that he represents his game first and foremost to fit the narrative of how the Mother protagonists work. They aren't just themselves. They have PSI from all party members. To make Ninten stand out, simply using his own PSI isn't enough. You already have your differences with Ness and Lucas to a big degree.
Here's one thing I don't like seeing; why should he get in just because it's the anniversary of his game. That's literally "let's add him in just for the sake of getting a Mother 1 character in". That shouldn't even be a reason. He's more than that. If he's so unique, he can get in on his own merits. Characters shouldn't be added just to promote a game alone. Also, there's no denying that Ninten looks like a slightly less detailed Ness, meaning a new design or enough changes is absolutely important. Besides that, Mother 1 was never on the table because the game wasn't relevant. It wasn't worldwide. Ness already did the job of representing the full series at that point since the gameplay was the same. It's why it's important that Ninten isn't just unique in some way(aesthetics alone is nice. See: Daisy), but it's also important to choose him because it feels like a reason to go for him. When you look at him, why do you want him? To have an alternate Ness-esque moveset that is more about Ninten than his party members? Because he's simply a protagonist?(Also, Porky is the antagonist of a game Ninten isn't in. That means you wouldn't be adding his antagonist before him. You'd be adding Porky after his protagonists he faces are in. So it fits that narrative fine. Porky coming after Ness and Lucas makes sense. He has nothing to do with Ninten if we care about protagonists and antagonists in itself. It should only be because they're connected via story. As you might notice, I was wrong on Porky. That also throws a flaw into what you said. If a protagonist should get in before their antagonist, that means that Ninten is not competition for Porky under that particular "rule" of yours).
I could go on, but the point stands that both Ninten and Porky are good choices, but they also have very different roles and reasons to be in. Plus, keep in mind some want more villains in because they like the interaction of Heroes VS Villains. It's shallow, perhaps, but it makes sense. Many games have a good and bad guy. Smash is full of bad guys too. Having one's villain makes Smash feel more complete. I won't pretend it's the best reasoning in itself, but it's a bit better than simply "we must add every protagonist before any villain", really. That's not a good narrative. I agree it makes sense the player character, which is always the protagonist of the story, should have normal first dibs over the antagonist(note, I don't mean Hero and Villain here. You can have villain protagonists too). However, one thing should be noted that Mascots also can have higher priority over the player character/protagonist as well. Pikachu is proof of that. In certain games, the best option can be the protagonist or mascot for first dibs. You have to look at the entire game and how it's played. You have to also take into account the Smash game. Trophies are gone. A game's lore is unlikely to be as notable now, so a protagonist shouldn't be added because of their lore itself. It's not really able to be translated into Smash. That might mean the mascot is the smarter first choice. So it comes down to moveset potential. That said, I think Porky would fill out the series better first, but Ninten could still work fine if they add both. I think an echo with altered moves so they represent his team mates might work best, with Porky being more unique. It's fine if you want Ninten more, of course. But keep in mind the flaw in you reasoning of "all protagonists before antagonists".
...Yeah, that's a lot to say.