While this is what I am afraid of (still not being particularly happy about her inclusion), I'm not sure the logic actually follows. Rosalina is still more relevant to the Mario franchise than we can say that Ghirahim/Midna is to the Zelda series. Rosalina has established herself as a character beyond the Galaxy series with Super Mario 3D World.
She looked to be a one-off character, but Nintendo decided otherwise.
A Fire Emblem Awakening character is likely to begin with, because the franchise is entirely different in characters. The vast majority of new Fire Emblem games have a new main character, thus why Ike was in Brawl, although he hasn't necessarily set himself up to be a recurring character in the FE series to my knowledge. The same logic very much follows with Roy in Melee.
Seeing as one-offing is kind of the nature of the FE series (correct me if I'm wrong, though, I haven't played the series extensively), it makes sense to do the same in representing the series in SSB (save for Marth, who is the original FE lord).
Zelda is entirely different... The same main character every game. The same princess. And a very prominent villain that appears in most titles.
Zelda has entirely one-off characters in a technical sense. Does the Link from Ocarina of Time live in Twilight Princess?
(He actually sort of does, but that's never even implied in the game itself) No.
Link, Zelda, and Ganondorf represent game elements more than they do actual developed characters. The actual characters in that sense, Midna, Ghirahim, Medli, many others, they never appear again, because no Zelda game is really set in the same time. As stated many times by the creators, Zelda's story/canon is completely an afterthought.
However, Fire Emblem's story is more "realistic" so naturally the main characters of the first Fire Emblem don't appear in the thirteenth
(one actually does but she is a dragon)
Which brings me to Mario. A series that literally could not care less about story. Naturally, if a well-received game has a well-received character, they're going to use them again because they can. Rosalina was almost non-existent in SMG2.
She only appeared in spin-offs. She appeared playable in SM3DW, but that was made by the same team as Super Mario Galaxy and had a whole world inspired by it.
The point is, Super Mario Galaxy,
one successful game, along with obvious potential, got Rosalina in Smash Bros.
So it isn't impossible for the same to happen with another character, a good example being Midna as she falls under a similar situation as Rosalina but also appears in a series with mostly non-recurring characters.