As someone who loves both Fire Emblem, and Legend of Zelda, I definitely agree that both are poorly represented, and one is under represented.
Sakurai didn't even plan to add Corrin. In an interview, he stated that the only reason Sakurai went with Corrin in the end is because of a lot of the people who were working on Smash practically begged for him to put Corrin in the game as DLC. He feels there are already too many sword-wielding Fire Emblem Characters in Smash. . . Which is probably why he made Corrin so much more unique and different from the other Fire Emblem characters on purpose.
As for Legend of Zelda, I definitely think Sakurai is going in the right direction for representation. Keeping the character designs from all sorts of games, with Zelda representing aLBW and aLttp, Ganondorf representing OoT, Sheik representing OoT and BotW, Link representing BotW, Toon Link representing just about any and all the games that feature the Toon-esque art style (which is a massive amount of them), and Young Link representing OoT/Majora's Mask. The only thing to take this a step further is adding a character that isn't a triforce wielder, who is already immensely popular.