If I were doing it I'd:
-Have enemies drop rupees & hearts like in traditional Zelda games
-Have shops in towns where you can buy things with rupees instead of just having obligatory freebie health and magic healers in each town.
-Falling in pits/water/lava would return you to your last safe platform with hearts removed instead of a death
-Remove the whole lives system. Starting back at North Palace each time is pure tedium with no gameplay benefit. The life system makes later palaces an enormous ordeal to get to, and you have to hope you didn't randomly take too much damage along the way to the palace, because otherwise you might as well just reset.
-Get rid of weird one-offs like slashing your sword under a table in a particular house to find a missing item.
-Replace and rename some of the spells. Like the "Spell" spell that gets used just once to reveal a hidden door on one screen. That should be renamed or remade into a magical item, and it should be useful in more than one situation. Reflect spell, Fairy spell, and Thunder spell need work as well
-Have shield spell last for a timed duration rather than just until a screen transition. Better yet, make it an item, like a tunic upgrade.