I played the system for a few more hours. My wrist stopped hurting and it didn't give me anymore trouble. However, no matter how much I tried to experiment with the 3D settings, it just constantly looked like a blurry mess. My eyes are pretty bad and I have high strength prescription glasses, so I'm not sure if that is throwing everything off. I don't think it should, but... it might? The games just looked better with the 3D turned off.
Really liking Pokemon so far. It's pretty addictive. Animal Crossing was fun, but then the shops closed and I literally can't do much of anything until tomorrow.