It's not backwards when you take into account that there's two different fanbases. You have the fanbase that actually knows about her and want her in for her own merits and then you have the fanbase who doesn't know of her. If Sakurai thinks she can get into Smash Bros,, for one reason or another, then the fanbase who doesn't know about her learns about her, some or most get interested in her which eventually turns into more popularity and because the one fanbase is much larger than the other fanbase, her popularity basically becomes more than twice the amount then before she got into Smash Bros.
But then this goes to what SPEN18 was saying insofar as this really could apply to anyone.
That's why it's backwards. You're literally starting from the point that she's been selected and then saying that will get her popularity. You're starting at the end, she's already been chosen. But why did she get chosen? That's what you need to start with.
What, because Sakurai saw something in her? That could be used for literally any character.
The characters you mentioned before were chosen because they represent their whole series. She does not. If anyone were to do that, it'd probably be Shulk. Or, they were beneficiaries of good timing. Which she isn't. That's why as parallels, the only thing they share is maybe they weren't so popular beforehand. But that's a negative. That's a deficit they worked around thanks to their positives. But the positives they had, she lacks.
Also, Elma is absolutely the main representative for Xenoblade Chronicles X, much like the Fire Emblem protagonists for their respective games, Ness for Earthbound and Lucas for Mother 3 and Shulk for Xenoblade 1 and Pyra & Mythra for Xenoblade 2. She is the main character next to Cross in Xenoblade X and plot and story-wise, she is easily the most important character of Xenoblade X. She was also used for representing XCX when she appeared in Xenoblade 2 and she still appears in artwork regarding Xenoblade X, like the Monolith Soft compilation artwork or whatnot. So she certainly does not lack being a representative of their series, but as you said, it's really just timing that she's not in.
Of course she represents her game, but that doesn't really matter if XCX isn't the current, new title. If FE7 were to get a character it'd be Lyn, but it's not going to get a character over Engage or whatever the newest FE would be. Even if we get that FE4 remake, new games still seem to supersede that. If we got Gen V remakes, it wouldn't really matter who would get picked there, because we'd get Gen IX or X.
Ness, Lucas, Shulk, and Pyra/Mythra were all the current characters at their time of selection. It's either going to be that, or characters who front the whole series like Marth or Cloud. Elma does not play that role in Xenoblade.
It'd be a different story if the only thing we got after XC2 was this port. But hey, if XCX2 comes out, and Elma retains her prominence, she'd be in a very good position so long as it remained the current one. Which would be cool, I'd prefer Elma over Noah or Mio.