Eh they have kinda had a 3D pokemon game. One of the pokemon stadium games actually had a story mode where you walked around in a 3D world, could catch pokemon, battle ect. The whole game was done in double battle format and instead of catching pokemon in the wild you would occasionally see a trainer with dark pokemon that you could catch and convert into a normal pokemon.
I loveeee it :$ Can i ask you something? -Pleaase do it <3 ;] can you make some more like this :$ I'm totally addicted to eevee I have a few examples [in case you have no ideas anymore] air and like the pokemon kitty (candy?) and those were my ideas XD BUT. if you don't want , i understand that