Pokémon can and will survive no matter what platform Gamefreak want's it to stand on. While the 3DS and DS(i/Xl/etc) present their own positives and negatives, it is important to note that a move to the 3DS - especially mid-generation - may not be economically viable, as not many people have 3DS's yet. Personally, I believe that once the 3DS receives an upgrade, (akin to the original DS's DSi) then Gamefreak could consider making some games with features exclusive to the 3DS.
If I recall correctly, Gamefreak announced that there would be 3DS exclusive features, but it wouldn't be mandatory, if you will, to have a 3DS. I'm not sure what these features would be, and how they would be implemented, and I'm not sure it's the right place to discuss it here.
I would like to see, personally, the 3DS to be upgraded with better graphics, and in turn the Pokémon series to be upgraded with better graphics onto the 3DS. However, I think that Gamefreak/Nintendo will be looking to put the third installment of Black and White on the 3DS, and possibly the Ruby/Sapphire remakes as well; but no matter what they do, they are always going to have fans that will play and buy their games. That being said, some people still haven't bought a 3DS (me included), and I will not I would probably buy one just to play a Pokémon game, if it comes to that.
EDIT: Realised that I had read something written by a fan, not by Gamefreak, and my memory somehow screwed it up. Aploogies.