This page explains how to get all of the upgrades in the game for arrows, bombs, wallet, and magic meter.
Magic Meter Upgrade
There is only one magic meter upgrade. To get it, you must have the boomerang, although it is easier if you have the cannon. Go to Two-Eye Reef and defeat the Big Octo there to receive the magic meter upgrade.
One of the wallet upgrades is on Outset Island. You have to have bombs to get it. Use the Deku Leaf to float back to the cave where you rescued Tetra at the start of the game. Inside, use a bomb to break the large rock. Drop down into the hole and talk to the fairy to get the wallet upgrade.
The other wallet upgrade is on Northern Fairy Island. Drop into the hole in the shell and talk to the fairy to get the upgrade.
One of the bomb bag upgrades is on Southern Fairy Island. Use a bomb to break open the door, drop in, and talk to the fairy.
The other bomb bag upgrade is on Eastern Fairy Island. Bomb the rocks, drop into the hole, then talk to the fairy to get the upgrade.
One of the quiver upgrades is on Thorned Fairy Island. Use the hammer to pound down the stakes, then drop into the hole and talk to the fairy.
The other quiver upgrade is on Western Fairy Island. Use the hammer to pound the stakes, then drop into the hole and talk to the fairy.
To learn the hurricane spin, give 10 knight's crests to Orca. You can use the grappling hook on Darknuts to get Knight's Crests.
To receive the Magic Armor, do the merchant quest until you receive the pinwheel. Then talk to Zunari to receive the Magic Armor.
Give a total of 50 Joy Pendants to Mrs. Marie in Windfall to receive the Hero's Charm. Equip it using the Quest Status Screen. It allows you to see the life meters of your enemies. You can get Joy Pendants by using the grappling hook on bokoblins.