Some of us like F-Zero you know
This. A major reason I play Captain Falcon is that F-Zero is one of my favorite video game franchises, not because I think Captain Falcon is oh so funny (although I do think his moveset is delightfully over the top).
I think one of the chief goals of Smash should be to include a great cast of playable characters from as many of Nintendo's major franchises as possible, regardless of how great they've done saleswise. Each and every franchise represented in Smash meant a lot to
somebody, so it's great that they all have reps. Yes, F-Zero is usually a sales disaster, but I have picked up every game in the series and loved them. So yes, millions more people love Zelda and will play as those characters, but that doesn't mean we should just cut characters from other series.
I don't know. I've just never wanted to cut any characters. Frankly, for example, I like Zelda and Fire Emblem way,
way less than F-Zero, Mario, Pokemon, Pikmin, etc, but never has the thought crossed my mind, "Gee, I wish they'd cut these characters
I don't care about." I realize Fire Emblem and Zelda characters mean a lot to some people, so that's enough for me. What's more, they bring characters with new movesets into the mix, which makes things more interesting.
Also, just for what it's worth , I don't understand why Ganondorf is a clone of Falcon. He's been a boss enough times that Sak could just pull moves from actual Zelda games to make his moveset rather than cloning him from Falcon. Falcon's moveset is cool and unique, and because he doesn't have a moveset from his own games, changing him would be more of a task. If anyone's moveset should change, it's Ganondorf. Having said that, I don't really care if Ganondorf doesn't change either. He's still different enough to be interesting.
Edit: I'd also mention that Pikmin 3 came out about 9 years after Pikmin 2. You could argue that if Pikmin 3 had never come out, Pikmin would be slipping into irrelevancy, but that wouldn't mean Olimar wouldn't have a place in Smash. He was a character from 2 games that a lot of people loved, and he had a unique moveset. That's all that matters.