Guaranteed 3DS, with a small chance of a less refined version for the DS; e.g. less features, worse graphics, etc.
History begs to differ. Aside from Crystal, every other 3rd game has been on the same system as the first 2. It makes no sense to put the 3rd game onto a new system. Why? Lets look at it logically:
1. The first two versions were on the NDS, and since GF has a habit of making the third game able to interact with the prior two, it stands to reason that they will put it on the same system.
2. Since the 3DS is still new, GF would be hesitant to put the third game onto the system, since it could potentially lower their fanbase. That is why when the Wii first came out, Nintendo still published Gamecube games. It is the same reason why there were still GBA games coming out when the NDS was released.
3. The system servers would be incompatible with 3D sprites. You cannot transfer a 2D object into a 3D environment without specific programs and commands, which can take over a year to complete. The same works in reverse.
4. The output files would be different formats, and thus unable to be transferred to older or new games. This means they would need to make so sort of "Pal Park" program to transfer Pokemon from NDS games to 3DS games.
5. The time it would take to encode everything from the NDS file formats to 3DS file formats would take the better part of a year, because of different commands and dimensions.
With all that in mind, it is much easier to do as they always have and use the codes they already designed on the NDS, and build around that. Also, before anyone mentions the old Coliseum games that used the GB games, you must remember that those were console games, and had build in codes to render the pokemon from set codes and commands.