I agree. Don't get me wrong, I'm happy the series is moving forward. I'm not gonna be one of those guys whose like "We should have sprites forever!!!"
But ever since Gen 1 with Stadium or Snap or whatever, we've always had both 3D models AND Sprites for Pokemon, and it's a little sad to imagine we might lose one of those forever.
I'm really hoping the game will have sprites in some form. Like maybe a special mode of the Pokedex or PC will let us view them as sprites, or maybe the Party Menu Sprites will be like Gen 5 equivalent or something.
Worst case scenario, I'm pretty sure fans are already drawing sprites of all the characters and Pokemon, and they look alright. But it won't be the same.
Don't forget to check out my MegaTen themed webcomics at http://www.drunkduck.com/user/Strain42/ (Currently Updating: Persona 4TW Add-On M-F)