>>54158856-Square-Enix owns the trademark
-Game Freak has a high turnaround, so even if they hire talented dot artists, they're more likely to be headhunted for higher pay by another studio after one game
-2D isn't the industry standard anymore, it's more for niche and specialty projects. Japan puts more care in dot graphics than the Indie guy who can't draw for shit or repaints Mega Man sprites so no the Mojon Twins and the Renegade Kid developers don't prove shit.
-Game Freak is informally a finishing school for game dev graduates, so it makes more sense for them to tow the line of today's standards than it does to make a supposed passion project for 2D Pokemon, which they weren't even that good with 2D to begin with. People just flash the halo effect on their 2D days because their favorite Pokemon posed better in 2D due to exaggeration 2D offers or some shit. 3D has its problems but there's always new ways to handle, scale and update 3D models seamlessly whereas 2D is more the labor of drawing new frames of the same character.