I don't think the main issue have with glasses is having to wear them, more the fact that *every* person in the room needs them, and at 80-100$ a pair basically fucks you over if you have any reasonable amount of friends (unless your loaded like fuck). Saying that unless your loaded as fuck your not going to be able to afford 3D tv any time soon, so the point is kinda moot
Bringing up the 3DS, I'm guessing its going to use the same technology as is used on FinePix REAL 3D W1 camera, which is basically a prism film over the screen to create the 3D effect. There was also a phillips TV at CES2010 that used the same technology on a larger television screen I believe, and allowed 3D images to be seen without glasses. The downside however is that you need to be directly in front of the screen at the right distance or you don't get the 3D image effect.
Of course for handheld gaming distances are normally quite close, and it nearly always going to be held directly in front of you, but I'll wait to try it before saying it'll be a success. If the distances and angle for 3D don't allow a fair degree of movement, I cant see it being too big a hit.