I think 3rd party characters need to have the benefit of nostalgia moreso than 1st or 2nd party characters. Sonic, Snake and Mega Man all have HUGE fan bases and people who think fondly of them. Even appearing in general pop culture.
I don't think Layton has that historical or cultural appeal to warrant a spot on the roster. That's the one thing that really skewers his chances. It doesn't help things that he seems to be a pacifist. Of course Villager is a pacifist too but he can go down the mischievous antics route....Layton can't go down that route because he's a fairly serious character.
I think that bodes well for Layton. It'd look old fashioned, backwards-thinking and samey if every third party was retro. Layton would ad variety and show that Nintendo still has stuff to offer in the way of big exclusive third parties. And I mean, I genuinely can't think of more commercially and critically successful third parties that are as well known as Layton that are exclusive to Nintendo for many years. in fact, I'd say there aren't that many in general from recent years.