You know, I've noticed this. Kid Icarus was treated like an "Original 8" franchise at E3 2013, and Pit is getting a pretty big influx of content in this game. Not really accounting for the fact that Uprising came from Smash and Smash Bros. made Kid Icarus what it is now, more or less. But look:
Mario / Luigi / Bowser
Donkey Kong / Diddy Kong / K. Rool
Link / Zelda / Ganondorf
Samus / Z.Samus / Ridley
Kirby / Meta Knight / King Dedede
Fox / Falco / Wolf
Pikachu / Whoever / Mewtwo
With Ridley, Mewtwo, and K. Rool as possible and very popular inclusions, every Original 8 franchise except for Yoshi has at least three characters: The protagonist, a major side character or secondary protagonist, and a major classic villain.
Besides that, with Palutena being a "popular" choice and Medusa being a "unique surprise" choice, Sakurai could add both and make a pretty significant number of people satisfied AND give Kid Icarus a good amount of representation in Smash. While I think he would go with unique over popularity for this game, I would think Sakurai knows one of the big things about Medusa and Palutena is their own character conflict with each other. Besides that, he probably also knows that this could be the last chance (or rather, the best chance) for this level of Kid Icarus addition to Smash Bros. since really, who knows when we'll see another Kid Icarus.
Just what I'm thinking lately.