May or may not change how Showdown and PO look. Honestly, I don't care about the graphics, cause this is 3ds, and everyone knows handheld consoles are less powerful than home consoles and it's just a load of blasphemy. Although, I must say that it looks quite nice indeed, and looks VERY interesting.
Anyhow, unless PO and Smogon want to make sprites for all the new gen pokemon, then they're probably gonna have to revamp the whole thing with the sprites.
Why are you so interested in that though? It'll just look the same as the games xD;
but I guess people will need stronger computers to support the graphics. I'm sure there can be a 3d effect added but it'll just be hard to do. It might just be easier to make sprites for all the new guys. It'd probably be easier for everyone. But I don't really know much about it, that's just what I THINK, I'm not all that sure about it all.