The thing is, they'd have to make 3D models (like those in Pokemon Stadium, etc) for all of these Pokemon and format them into the game. Not only is this extremely difficult, it takes a LOT of time. You have to realize that The 3D Pokemon games like X and Y, Colosseum, and Stadium were made by paid professionals and took years to make and develop. Now, I'm not saying that these guys aren't professional, but it's just not worth it to craft all of these 3D Pokemon and set them out for free. Not only that, but they'd probably have to remake the whole game in 3D, so the models wouldn't stand out. Someone will probably take on the challenge some day, but don't count your chickens before they hatch, haha.