Hell, it gets even weirder; for Pokemon, it has 3 core mainline series(regulars, remakes, Let's Go), and the Legends series as well(I don't remember if it's supposed to be part of the regular or remake universe, though).
Mainline also doesn't equal canon in itself. Sonic has a ton of canon spin-offs(Shadow the Hedgehog, Sonic Battle, for instance). It's actually about the genre, though that can vary anyway depending upon the Developers. Ultimately, the Developers are the only ones who decide if it's mainline or not. I absolutely think it's really weird that Super Mario Bros. 2: The Lost Levels isn't mainline, but they don't count it(this could be because Super Mario Bros. 2 USA stands out better and the other feels like more of an add-on to Super Mario Bros. instead of a full sequel. General full sequels do tend to heavily change it up a lot more. Even then, The Lost Levels is pretty early in the franchise. ...There's also some idea(I'm not sure how confirmed it is) that Miyamoto dislikes the game, which could also be why).
Though more on the Super Mario front, I've read some fun stuff; The King in the old Super Mario Bros. Movie is named Bowser in the original scripts(after two renames), and outright directly in the Novel. Funnily enough, Bowser in the games became more amicable after the movie was released(the Novel released the same year too). In fact, Super Mario RPG came out quite a bit after too. Another fun thing is Miyamoto legitimately liked the old movie because it didn't try to play it safe overall and did its own thing.
Anyway, Echoes of Wisdom is officially mainline. That's all there is to it. The real question is is if they consider remakes as important as the originals in a similar way that Pokemon does.