First off, I think you did a good job making it feel like you're in the video game universe.

Why is magic points derived from courage or wisdom? From wisdom i could see, or from all three, but i couldn't understand why courage or wisdom. Ganon had the Power triforce and he did magic constantly.

Can garudos rest without food or water for a week? That seems weird and out of character for them.

I feel like HP and MP, and ammunition should be able to be increased during battle and while adventuring, not just while resting. I might suggest adding a system of having containers during adventures and fights which can be broken to gain their insides. With that in mind, you could add abilities/weapon types that are specifically good for harvesting these in combat. (Sword spin good for grasslands, etc)

Armor and shields made my eyes glaze over and I didn't read it, much less understand it. Might want to simplify it or present it in an easier to understand way.

You really should explain what each item does. For example, Does a hookshot allow me to stun enemies, or does it launch me towards enemies, or does it drag enemies towards me, or can I grab their weapon, or...
For magic, how did you miss enchanted arrows? That should be the most obvious.Nayru's love is straight up broken. In general I think magic should be overhauled. Less like D&D and more like zelda.

Hope that helps!