It would be just as weird as having a game like Mario and Luigi: Bowsers Inside Story or Mighty Milky Way on a system capable of 3D graphics. Sprites are a design-choice, not the natural evolution of a game.For me, the Gale of Darkness image shows what pokémon will become, sooner or later, i guess later, but in a handheld that focus on 3D effects, it would be pretty strange,to have a pokémon with 2D sprites. Don't you agree?The overworld is one of the things in Pokemon that I don't want to change. The current overworld is practically perfect. The 3DS version would just help perfect the aesthetic with increased screen-real estate and better 3D graphics in the few places that it's actually used in.
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Just look at XD: Gale of Darkness vs. Black and White.
http://i.imgur.com/jmBen.jpg
http://i.imgur.com/LZxTo.jpg
The top looks bland and uninspiring while the bottom has this great look to it. The sprites just add to the great aesthetic that the Pokemon series has. And as an added bonus, games that use sprites tend not to age as horribly as games that don't.
Pokémon Stadium proved how good battles in 3D can be.
It's not a fact, it's a personal thing, but the common sense tells: Pokémon battles in 3D is better than 2D sprites.
I think that sooner or later we will have battles in 3D on 3DS, and I think the 3DS pokedéx is a preview of what it will be.