The difference with Geno is that he doesn't have much of a presence even in his own franchise. Geno was a one-shot character who wasn't even the main protagonist of his own game.
While Fire Emblem definitely has a lot of one shot characters, they also added...
Ike- Main protagonist of two major Fire Emblem titles.
Robin, Lucina, Chrom- Main characters of the game that pretty much saved the franchise and is arguably the most successful title in the series.
Roy- Okay, I'll give you Roy. I don't think he was worth adding. He's in his own game, and to my knowledge, FE6 isn't exactly a fan favorite compared to other games in the series. Educate me if I'm wrong though.
I don't know enough about Corrin to have an opinion on him/her.
My point is this. As cool as Geno is, he isn't super important to the Mario franchise as a whole. (Most of) the Fire Emblem characters you're talking about are still very important to the franchise as a whole despite only appearing in a few games.
I like Geno and I'll be happy if he gets in, but I'm not holding my breath for him. But who knows? They added a generic piranha plant. We could get Geno and Mallow a couple of months after launch for all I know. Sakurai's just doing whatever he wants at this point.
in the polls genos one of the most popular characters in one of the best of the mario rpg games. hes also a mark of the first collaboration with square, which is odd that cloud made it in before him. but its not like importance is what makes him choose the characters. the ice climbers are literal who characters from a game back in 85, rob was a toy that was issues in early runs of the nes thaat was eventually phased out to the point that most nintendo owners have never owned one. and then theres characters like lucas that have games that have never left japan. piranha looks fun, and richters in so unless hes for some reason trash im gonna use him, but its apparent that sakurai loves fukking with the fans of this series first and formost