Yep, this is what I do.Sometimes I turn on the 3D for like 20 seconds then turn it off.
Some events with animations really look good in 3d so that's the only time I would turn it on.
I think the 3D looks really nice, but finding the correct angle to tilt the DS isn't convenient, and if I look at it for too long my head feels funny. Mostly I can't (and don't) play with 3D on because of the angle issue.
I flip the 3D more often while playing Japanese adventure games/visual novels, because there isn't pressure to react quickly.