Don't ask me for the exact news this was mentioned, but ED said the speaker hole design is pretty much fixed as it's designed from the speaker manufacturer specifications to get the best sound out of it.
If that's the case, don't change them at all. Function over Aesthetics (EXCEPT FOR THE DPAD!!! B) )
Oh, and I just realized, we can just bloody open up the case ourself and rearrange the ABXY buttons! Stupid me, why didn't I think of that. Just be sure that the software has some kind of option to have that work out better.