To be more honest, Wolf has done more for the series. When he first showed up in Star Fox 64, he brought along a memorable team that was, while a cheap knockoff of the true band of mercenaries for the Lylat System (Star Fox), Star Wolf has been memorable to the series. Krystal has a lot going for her as a love interest to Fox, but I can't help but feel that Wolf has seniority over her when it comes to significance. It would seem that Sakurai and his team feel the same.
Falco? Of anyone of Star Fox, or the entire series of games, he is considered the best of the best. He's the Ace Pilot of Star Fox, and practically like a first mate for the team. If they were ever pirates, you can count on Fox being the captain with Falco being the first mate. Not exactly a side kick, but relatively close enough. He's also been there from the VERY beginning. There hasn't been a single Star Fox game that he's missed out on. Not even Star Fox Adventures where he helped you defeat Andross in the end. This homegame popularity, coupled with his Smash Bros. popularity is more then enough reason for him to make a return over Krystal and even Wolf if it came down to that.
Would I be happier with Fox, Falco, Wolf, AND Krystal in Brawl? Of course I would be. But who are the more important ones? Fox, Falco, and Wolf; this is just my opinion, remember that.
Who needs a triangle just because the series usually has a hero, a villain, and a damsel in distress? Pokémon didn't get this and it's one of the biggest franchises in the world. So where's Mewtwo or even Misty while we're at it? Get what I'm saying?
I'm happy with Fox, Falco, and Wolf. And I would have wanted Wolf & Falco over Krystal in anycase. This isn't because a dislike for the character, but Wolf feels more significant to represent the series, in my opinion; the same goes for Falco.