I think I may be the first one to say that I play this game on 3D all the time! I tried playing it in 2D mode, but i don't find that as engaging... I don't know, there's something about the 3D that just captivates me. It makes me feel more drawn into the world, as opposed to making me feel like I'm playing a video game.
I take my 3DS with me to school, and I'll play anywhere between half an hour to two hours, depending how busy I am between classes, and I always get home with more than half of my charge left. Maybe I should experiment how long I can last with the 3D off. I usually play with the brightness set to 3 or 4 with power-saving mode on.