Dust319
Smash Apprentice
Peach and Zelda were chosen because they are 3/4 of the time crucial parts to the plot.
Zelda- because she is the bearer of wisdom. Without her, the legend of the triforce would be incomplete. Most Zelda stories revolve around the Triforce, and their 3 bearers. The Hero, the princess, and the Dark King.
Peach- Most Mario game wouldn't have taken place without the kidnap of Peach.
Krsystal is not as important to the starfox franchise as Peach, or Zelda are to their respective franchise. Wolf is arguably considerably more important to Starfox.
Can I qoute for truth? Can I really do that? Ok.. QFT
The fact is that Krystal is relatively new to the Starfox franchise, and as of Command, her relationship with Fox is up for question.
That having been said, I think the Smash team decided to go for more of a Ryu, Ken, Akuma triangle, rather than a representative triangle like other series. Fox is typically the hero, he's your "Ryu". Falco is a pilot of similar or equal skill to Fox, so he's the "Ken." Wolf is the evil counterpart to Fox, so he's your "Akuma".
Come to think of it, I think Starfox is the only Nintendo series I'm aware of that is capable of this type of triangle, which makes it far more representative of the series of a whole. And that's my two cents.