Easily Improved Point 1: Fi. Fi is a sweet concept, giving the Master Sword itself a personality, which gave the sword that's accompanied Link a deeper connection. It retroactively makes the Master Sword in the other games cooler, because now it's not just a weapon, but an eternal companion.... THAT WON'T SHUT THE FUCK UP, JESUS CHRIST I GET IT THERE'S A 95% CHANCE THAT THERE'S A FUCKING MOUNTAIN IN FRONT OF ME! SHUT THE HELL UP!
So, easy fix, you can already talk to Fi at will, right? Maybe one of those dialog options is, "Hey Fi, I know what I'm doing, mkay?" or "Hey Fi, I'm a little lost, can you point me around a bit?" Make all of the annoying "MASTER THERE'S AN 85% CHANCE THAT THE THING THE GUY TOLD YOU TWO SECONDS AGO IS A THING" optional, through a simple dialog, and bam, Fi goes from annoyance to cool dancing robot sword lady. Problem fixed. This is especially easy, because most of the time Fi isn't even a part of the fucking conversation she's annoying you with -- she's just throwing a second unskippable conversation where she just repeats the thing they just told you. Would take very little reworking/effort.
Also included is not opening a slow ass dialogue box every time you walk over an acorn, and other slow ass dialogues.