You're right. I just tried the 3DS version and it indeed looks fantastic, but the sound on the latest release from 2015 is really bad. I tried the March 2016 build that someone linked saying that it's the best, but it still has problems. It sucks that it has those issues because picture-wise it really is probably the best option, especially the latest release from 2015 which on the top screen with 3D on makes the game and pixels look super crisp and bright.
Perhaps the latest build is better. Does anyone have a .cia of the latest one to try?