I'm not following, how would playing a (basically) DS game on the 3DS make it have better graphics? I'm saying, if Gray was on the 3DS and the DS, it could be the same exact game as the DS version except that it would have the option to play in 3D. And Nintendo has done something like this before. Look at the Mystery Dungeon games. Mystery Dungeon Red and Blue were the exact same games, with the exact same graphics, except the DS version allowed the use of two screens.
There's a lot of problems with this approach.
To begin with, the jump between the graphics the DS can do compared to the 3DS is a lot more significant between the GBA and the DS. Not only can the 3DS display detailed 3D (polygonal) graphics, but it has a much wider screen than the original DS does. If you just copied the way Pokémon games looked now and put it on the 3DS, you'd notice that the sides of the screen are filled with useless empty space.
Also, if you didn't redraw all the graphics they would look a lot smaller in comparison to the 3DS's larger, higher resolution screen. It's also worth mentioning that the graphics of the Pokémon games are not designed for the 3DS's 3D effects, and the game would require a lot of re-designing in order to properly take advantage of it.
Secondly, let's look back at Mystery Dungeon Red/Blue again. You noted yourself that they look almost identical and share the game graphics. Essentially, doing this would mean the 3DS game is incredibly crippled because the graphics are made with the intention of being able to run on a much weaker system too. Otherwise, if you go in with the intention of making new graphics just for the 3DS, basically they have to make nearly two games' worth of content, which means they'd be wasting more valuable time and money to make these games.
Most importantly it would look extremely bad for Nintendo themselves. Just being in 3D is not going to be enough of a selling point. If you tried to make a 3DS game with graphics that look just like a DS game not only would it receive a lot of criticism from pretty much everybody in the gaming industry, but it would hamper sales a lot, either from people who don't see the need in buying a $40 game that looks just like the one they have now, or don't feel that a game that looks so poor in comparison to everything else on the 3DS is worth buying.
DS sales would probably be lower than expected too because so many people already have a Pokémon game on the DS, there's less to incite them to buy another one than there would be if a brand-new game came out for the 3DS.
Mystery Dungeon got away with this because it was a brand-new series of games, so it managed to get by being a novelty and new approach to Pokémon. People have far greater expectations of a real Pokémon game, though.
edit: Wait, I forgot the most important part! Selling a Pokémon game on DS as well will do a great deal of harm to Nintendo's efforts to promote the 3DS system. Contrary to what some people might think, at the end of the day their main goal right now is to sell as many 3DS's as possible, using exclusives games like new Mario, Zelda and Pokémon.