In the transition to 3DS, Grezzo took some liberty to change a few things around. This page is meant to cover the more meaningful changes instead of the minor ones like text changes, unless the change adds considerable value with the new text somehow.

In the original Ocarina of Time, you could – if you were fast enough – re-bottle one of the three bugs when you dump them onto a soil patch to get the Golden Skulltula. Using the trick allows the player to only need to catch one bug in order to get the Skulltulas in the soil patches. It cannot be done in the 3DS remake, sadly.