Wishlist for 3.0 (if it's planned)
Opening cutscene. Pretty self explanatory.
Show the currently equipped item in the UI. Even if it has to take up a little bit more playspace to do it, it goes a long way into making it feel like on the the official games.
Knockback from contact damage, to prevent from getting hit multiple times in a row from one hit. Would also allow you to be a little more liberal with enemy collision, since it seems that some enemies can be practically stepped on without taking damage.
Better attack animation. At least a sprite showing Zelda holding the wand in front of her, ala Link's Zelda 1 sword sprite, instead of just the wand appearing in front of her idle sprite.
Wand animation for all of the spells. In theory, she's swinging the wand to cast them, so it should still show the wand.
Boomerang spell returns to the player. Even if the original game didn't do that, the boomerang spell should act like a boomerang. It should also carry items back to the player instead of collecting them on its own. You can probably cheat it a little by having it collect the items when it disappears instead of relying on the item contacting the player.
Sprite flickering. I know it's a controversial thing, but it helps readability if, say, you use the fire spell when you're on the same line as two moblins when you use it. Instead of making the fireballs invisible, make the moblins and fireballs flicker.
All in all, this is a really good fangame. And I'm honestly not sure which of these, if any, GB Studio would allow you to do.