How many people knew who Marthe and Roy were when Melee popped up?
Roy wasn't in a game yet, but Marth was always popular in Japan(which SSB and Japanese developers consider their main audience by tradition). Marth's game was the first RPG Strategy game ever(created the genre), the one of, if not the, first Strategy game on a console, and one of the most important strategy or RPG games of his era. Fire Emblem easily earns two more characters especially since they haven't touch polearm or axe users who are the rock and paper to sword.
Mother gets two characters because it's a new game setting(one villain aside) each time and both are major games on their own without being related(as opposed to Mario or Metriod where you are playing with and against most of the same cast). Fire Emblem too works like this too, cept it has 10 games(the one exception would be 3 which is a remake+more of 1). To claim Metriod had more effect is pretty out there... just because it was released in America doesn't really mean it had more of an effect than Fire Emblem. I don't think it didn't go as far to create a genre(and one that contains favorites Final Fantasy Tactics, Shining Force, and Orge Battle(s)
Anyway, to count game series:
Pokemon does end up having a lot more. I miscounted the Pokemon stadiums and stuff like Pokemon Pinball and Pokemon Box. However if you don't count silly spin-offs and only the Stadiums, Generation games, and Mystery Dungeon/Ranger it's hardly a big advantage over Fire Emblem.
Fire Emblem does dominate most other game series though. One thing to consider is that when you add Mario you represent every single Mario game. Same with Samus, Donkey Kong, and any Pokemon. You can't say the same for most Fire Emblem games with Marth the exception as he's the most popular and iconic protagonist of the series. Ike does represent two games though.
If they were to add Fire Emblem characters it wouldn't really be a sword user. It would be an axe or lance/spear user. You are only telling 1/3rd of the story with just swords. Roy was redundant and in comparison one of the least important/popular characters of Fire Emblem. His father Eliwood was much cool, but maybe even less important... his father friend Hector on the other hand... there's not a single Fire Emblem fan who didn't want him to show up in SSBB as he's basically the most iconic axe user of the series.