Fire Emblem, I can agree with. Way over-saturated in my opinion. Marth, Ike, Robin, and either Roy or Corrin woulf make for a nice four.
I'm going to have to disagree with you on Mario and Pokemon. I think the number of characters those series have is fitting. Wouldn't even mind it if, say, Captain Toad and Decidueye joined the fray. After all, Mario and Pokemon are two of Nintendo's largest series.
If there are going to be more Mario and Pokémon characters, then I expect equal promotion of other franchises. Popularity shouldn't be the sole reason for making new characters for those franchises every time. Super Smash Bros. isn't just about popularity, either. Who was aware of the Mother series, except the very few who played Mother 1 and 2? What was the demographic for Fire Emblem in North America before Melee? If anything, Super Smash Bros. introduces the unknown and the unpopular. There's no reason for the entire Mario cast to be in Super Smash Bros. Such numbers are incredibly high, as are the number of Pokémon in their own series.
Mario, Luigi, Peach, and Bowser are honestly the only characters necessary. And you could just drop Luigi if it had to be limited to three characters per series. With more characters, there's not enough time to develop characters in a balanced manner. The number of characters also affects the tier list considerably, since characters who would be low-tier in one game would likely be bumped up in the next. Consider Samus. She's 8th out of 12 in Super Smash Bros. Pikachu is 1st of 12. So 1-(8/12) puts her at 33%. Melee, she's 62%. Brawl, she's 16%. Sm4sh, she's 33%. (Miis weren't considered.)
So, Samus is currently in the same rank as she was in the original game. She's considered low mid-tier right now, likely due to the bigger roster. She was low-tier in the original. A big roster could bring a character up or down on the tier list. A smaller roster might not have as many characters as people might hope, but a smaller roster allows for a better balance. My opinion is unpopular, and if I had it my way, a lot of characters would be discarded and replaced. If popularity matters, then a lot of characters should be discarded anyway, due to their small fanbase.