There's no way the remakes will be 3DS
Theres nothing to gain from making MORE 3D effects.
The remakes would only be on the DS if they are part of Gen 5. If they go to Gen 6 next, which will definitely be on the 3DS, then they'll be on the 3DS too. However, as has already been said, the DS is pretty much over.
Plus it would make transfering your old pokemon from the advanced series a long tedious process.
If you get to keep your old Pokemon, does it really matter?
DS games are still being made, theres no reason to make every game exclusivley for the 3ds because the 3D effects will remove a large portion of customers that want new games but are to young to have a 3DS(like a kid is going to leave that slider alone just because the game tells him its bad for him).
DS games are fading away. Gen 5 being on the DS was somewhat odd in the first place, though understandable in a way.
The 3D is totally optional. Don't like the 3D, just turn it off. I doubt kids would stare into the 3D that long anyway, I myself can only stand it for a few minutes before it becomes a little annoying.
And having all the regions in one style (more or less) is much more promising in the longrun.
Does it really matter if all regions are in the same "style"?
Also note that there were Dsi only games but Pokemon never touched them.
They might make the spin offs 3ds but the main games use sprites and 3d makes sprites look horrible.
DSi and DSLite are over soon too, if not already. 3DS is now. And I believe the 3D world and sprite character combination looks pretty good myself. The sprites themselves don't have to be 3D.
Besides, if the remakes were to be made for 3ds then Black and White would have been for the 3ds as well (foollowing the patern, the remakes are the same type as the new Gen before them.)
You're assuming they will definitely follow this broken pattern. We expected Gray/Grey. Black 2 and White 2 changed it.
I highly doubt that they'll switch to 3ds for the remake of Ruby and Sapphire, if they switch at all. I don't see how the fans of the main games will accept the games looking like the stadium series all of a sudden.
"If they change at all"? I hope you don't mean that you think Pokemon will stay on the DS forever, because regardless of when remakes come, Pokemon and every other major Nintendo franchise that hasn't yet WILL jump to the 3DS.
Also, I doubt a change like that to "stadium style" battles would be received negatively. However, I read somewhere that Game Freak prefers sprites for the main series, so we may not even see the games change to that.