I don't think they ever stopped. We haven't had a 3D Mario set mainly in the Mushroom Kingdom since 3D Land (though yes, 3D World's Sprixie Kingdom ain't that different), and before that 64. I just think there's something... cozy, for lack of a better term (it really is what fits best,
@WestEgg) about Paper Mario's RPG-like take on the Mushroom Kingdom that I wouldn't mind seeing revisited again at some point, though on the other hand I wouldn't really mind if Paper Mario's version just stays as the sort of definitive version of it.
I also do like how TTYD does a decent job at selling Rougueport and the surrounding areas as a place that would feasibly exist not far from the Mushroom Kingdom. My only real problem with it is how disjointed it can feel. Four of TTYD's local chapter areas are reached via pipe in the sewers; PM64 only does this once (and, noteably, one magic door). For me, that had a substantial impact on how connected the world feels. Petal Meadows, Boggly Woods, Twilight Town, and Fahr Outpost may as well be in their own universes - which frankly kinda works for Twilight Town, but the rest I feel would be better served by a stronger connection to Rougueport.