Indeed, all three of the Xenoblade games are good (I don't see why this opinion is so controversial). They all have flaws and detractors, but every game has those. Overall, I doubt reception of X is a problem for Elma getting into Smash Bros.Xenoblade X is easily the best of the Xenoblade games so it just makes sense to have a rep for the game in and it only makes sense for that rep to be Elma.
I think people over exaggerate it's negative reception. It got a lot of extreme blowback from specific fans for not being exactly like the first game (while it does have its own problems) but the game is well liked by many, reviewed well, sold pretty well for a Wii U game and Monilith Soft likes the game and Elma. So I don't believe Xenoblade X content and Elma would be passed over because Sakurai thinks the game is bad or a flop or that no one likes it.
I hope Elma gets in.