- Heart Piece from shooting magical witch sorceress thing is replaced with a bottle
- Bombers locations changed
- Bombers Notebook is obtained earlier and differently
- Stray Fairy locations are different
- Odolwa battle has been changed slightly (haven't beaten Snowhead yet so I'm unsure if the others were as well)
- A lot of Owl Statues moved, but they're still in the general area
- Kaepora Gaebora is encountered as soon as you enter Southern Swamp, meaning the Song of Soaring is learned a lot earlier than in the original.
- Rainbow Stairs in the Astral Observatory are gone
- Deku Link now has a... thing on the back of his cap that comes out when he spins, which is what damages things (can't remember if that was in the original or not)
- Fishing Holes are added, and as a result, prizes for the "3-Day Games" are now Fishing Passes.
I'm sure there are more subtle changes, this is just what I noticed.