I agree. Pokemon deserves to have that much representation.
Whether or not Sakurai is biased towards KI:U, Palutena honestly deserved to get in. People all over the internet were asking for her before Smash released. Kid Icarus and Kid Icarus: Uprising were both great games too, so I'd say that Palutena 100% deserves her spot. On the other hand, Sakurai probably was a
little biased towards Dark Pit.
I love Fire Emblem to death. Awakening, Smash, and ORAS are probably tied for my favorite 3DS titles (don't make me choose one 'cause I can't). I can see the bias towards FE though, honestly. FE isn't exactly the most popular or iconic franchise, but it got 4 reps. I'm not saying it doesn't deserve 4 reps, but compare it to a more iconic series like Donkey Kong or Metroid. DK only has 2 reps and Metroid only has 2, while FE has 4. Sakurai has stated many times that he loves FE. Connect the dots.
Honestly though, it doesn't really matter. Dark Pit is cool and I don't mind him getting in the game. I like FE a lot so I like the characters a lot too. I'm just saying that Sakurai was more than likely biased in his choices in making the game. Definitely not a problem though (at least for me).