From the looks of it, the Pokémon models do look the same as the ones from X/Y.
I'm well aware it's Sakurai being biased. Honestly, I'm not surprised, since he did start developing Smash right after finishing KIU and likely had the game fresh in his mind when planning Smash and you know he likes to recycle his previous games' ideas. There are a lot of recurring elements in his games regardless of the series they're from.
He himself admitted he thought on a lot of ideas for Smash during KIU's development. Gameplay-wise, KIU feels a lot like Smash, with similar mechanics and pacing. It's basically Smash and a 3rd person shooter put in a blender.
Also, I don't think the Star Fox series has stuff that would fit in Smash Run, but I could be wrong since I never played a Star Fox game.
It's a mix of bias and easy to port stuff, but like @
Cobalsh
stated, there are other 3DS games they could have ported stuff from.