I play in 2D. Before, I always played in 3D for New Leaf, but I've gotten used to 2D. Also, 3D is kind of subtle and quiet for me. Plus, I play New Leaf for a long time (it's Animal Crossing.) so I get eye aches and all the latter.
I play with the 2D almost exclusively. I will turn the 3D on to look at cool or unique things, but I turn it off once I am done. 3D just seems to give me headaches.
I really, really like the 3D, but I usually play in 2D because I only have one plug near my bed and both my 3DS and laptop need to be charged pretty often, unfortunately. 3D also irritates my eyes a bit.
I like using 3D, but I play on animal crossing a lot! So charging is a pain in the backside, so I always use 2D now. 3D is cool and I occasionally do switch it on!