It wasn't flipped for me, as I was used to the Wii layout. Would have loved to experience it as it should be for once. They should have just made that an extra option for both modes.
It doesn't completely fix the caves, but you can turn down the brightness to near original-level in the options, which is what I did. Didn't have any trouble reading the Light Spirit text.
As for my complaints, I *****ed about these before so I'll keep it short:
-Link still doesn't respawn on...