As someone with perception-based glasses, 3D only works for me if I'm only wearing one pair of glasses... In other words, good job Nintendo! I fucking love the 3D on the 3DS unironically! In terms of 3D movies, unless I really want to "immerse" myself in a movie I'm going to love anyway and I have the bones to dish it, I'm completely indifferent to their overall existence... But, if you're only going to have the 3D version available to buy if you buy the SE version of the Blu-Ray release, then it better be worth it other than seeing the movie at home in 3D...
Other than that, I mostly go 2D because it cost less... and that's about it...