Not many DSi only games (as in, very very few especially if you discount DSi ware =p) and would make zero sense to exclude people who only have a DS but not the DSi people. As said, a non-handheld console is not happening; Game Freak develops only for the handhelds and have said on multiple occasions they don't plan to do anything on the Wii/etc either.
That leaves the DS and 3DS. The former is clearly being phased out with barely any games now made for it, much less ones that would be major sellers. So hence the 3DS is imo what it will be (and we know they got their hands on the dev kits for the 3DS nice and early too). Don't see why it wouldn't after all.