Saying that Layton's not a Nintendo character = Saying Megaman's not a Nintendo character.
Added to that, Layton has only appeared on Nintendo consoles without exception, he's not featured on Mystery Room or Layton 7, only mentioned...I mean, third-party spots are for honorary Nintendo characters, right? Layton fits the bill perfectly! Yes, he's much more significant to Nintendo than Pac-Man, Lloyd Irving, Bomberman and definitely Snake, and he fits perfectly on the cast full of colorful, interesting characters, he has potential for one of the most varied, fun movesets and Level-5 certainly considered Layton for Smash at one point (The whole Layton's Twitter thing).
I like to think Layton will be revealed either on the next Direct, or with the NA/EU release of Ace AttorneyXProfessor Layton. If he's making it into the game at all, that is.