Fire Emblem is character-driven, and every game has dozens of playable characters. It's sort of similar to Pokemon in that sense. The Legend of Zelda, meanwhile, is adventure driven game with only one real playable character throughout the series.
There's still a number of potential fighters from the Zelda series (Skull Kid, Ghirahim, Midna, Tetra, Impa, any of the four Champions, Tingle, Yuga, ect), but I don't think the reason FE has more is simply due to "bias". LoZ already has its main protagonist (Link), namesake (Zelda) and it's main villain (Ganon), but FE is in a weird spot where it has several main protagonists and ultimately only some of them can be playable. It's why that despite all the characters FE has, there's still no villains from that series, despite having several notable ones (namely The Black Knight). LoZ is a "completed" series representation wise and any more characters beyond the main three would just be nice bonuses, while FE will realistically never be "complete".
I do think it's really strange how LoZ hasn't gotten a single newcomer in Smash 4 though. I'm expecting something in Ultimate, even if it's not until DLC. Even though I don't think LoZ needs any more characters it's kind of strange to see them not capitalizing on its popularity more.