Well if history is any indicator we'll get remakes for R/S for the DS and then a bit later we'll get grey on the DS as well. So no 3D capability until generation six which makes sense from Game Freak's point of view.
I'm basing my estimates because the DS was released in 2004 and yet Game Freak released Leaf Green in 2004 and Emerald in 2005. They did this to take a final pile of cash from gameboy users who hadn't bought the DS yet, and since not many good GBA games were being released since everyone was focusing on the DS, Game Freak made a lot of money. And at the same time Pokemon fans who had the DS could still play those games, so more money.
I think they'll try to use the same formula now because the 3DS hasn't been out long enough for Game Freak to develop 3DS pokemon games, instead they'll make these games into the DS because that way they will be able to sell more with less work since they don't have to work wiith a new technology, it is just basic efficiency. That way they can also tap into both 3DS and DS markets because honestly no Pokemon fan is going to refuse to buy the game just because they're not in 3D. If they made a 3D game many people wouldn't buy it since there aren't as many 3DS's as there are DS's.
Later on when the DS is no longer the largest consoled played or at least no longer the main nintendo console (as far as games produced goes) then they will release the sixth generation with 3D capabilities, this allows them to make money while they extend the time they have to become familiar with the 3DS and deliver a better game. Just like they did with Pearl/Diamond which weren't released until 2006 in Japan and 2007 in the US.
All I hope is we get better pokemon than in generation 5 because god most of them are so ugly. Game Freak you have years to design these creatures, please do it properly otherwise just gives a game with no new pokemon. Also not so many legendaries, remember when there wasn't 17 legendaries every generation...
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