Implement all the changes from the 3DS version, for starters.
Add a Light Temple dungeon. Getting the light medallion always felt anticlimactic to me. You get the Zora Sapphire, Ocarina of TIme, Master Sword, and Hookshot within 10-15 minutes, back to back to back to back.
Unfreeze Zora's Domain after clearing the Water Temple. Add vines to get back into the Ice Cavern after this happens, as the icebergs shouldn't be there anymore. Put the piece of heart that was on the iceberg at the bottom of the lake, possibly move the one that's already at the bottom of the lake, or just have them both down there for comedic effect.
Sandstorm in the wasteland should go away after completing the Spirit Temple.
Do more with the spirits in the Bottom of the Well. We see the spirit escape the well and go into the Shadow Temple, but that spirit is not present in the Bottom of the Well dungeon at all.
A way to change from adult to child on command, like the mirror from A Link to the Past.
Allow us to beat the postman.