Ocarina of Time is not only my favourite Zelda game but it is also my favourite game of all time. So with that being said, I don't think a lot of the game needs to be changed. Although there are a few aspects of the game that should have been changed in development.
- Rupees/ there should have been a larger wallet or maybe even a larger quiver and bomb bag so you could buy more arrows and bombs and actually use your rupees. There should have been more things to buy in general so the wallet wouldn't fill up so quickly.
-Warp points/ I found it annoying how there was no warp point near Jabu-Jabu or Gerudo Fortress. These areas both take a while to get to and it was just annoying how there was no convenient way of getting to them.
-Useless items/ I really do wish that the ice arrows had at least three or four uses. It's said that they were put right at the end of the game.
-More sidequesting/ I'm not too picky about sidequesting in OoT because it's my favourite Zelda game but I feel it could've used a little bit more like in MM or WW. Some more character development with the main characters and character interaction with NPC's would've also been nice.
Ocarina of Time is pretty much perfect though so I can't complain.
Things like better graphics and an orchestrated soundtrack are obvious, but I think the question is leaning more towards how Ocarina of Time could have been better when it was first released. Skyward Sword was my personal favorite Zelda game, but I still hold Ocarina of Time as the best. Skyward Sword is immense fun playing through, but it leaves me feeling like so many things are missing by the time the credits roll. Ocarina of Time doesn't give me that empty feeling, as it's essentially the most well-rounded Zelda game with the fewest glaring flaws and omissions.
Therefore, my list would resemble this:
#1: Make Epona more mobile. She couldn't touch water or hop down ledges, the jumping mechanic was a little gimmicky, and you could really only use her in Hyrule Field, Lake Hylia, Lon Lon Ranch, Gerudo Valley, and Gerudo Fortress. She was severely limited and a little hard to handle at times. It would have been nice to take her darn near everywhere and perhaps fine-tune her controls in addition to enabling Link to take damage on her, meaning you'd need skill to ride her.
#2: Implement difficulty levels. Ocarina of Time was a pretty hard game the first time around, but once you understand the controls and the enemies, it becomes pretty simple. A difficulty mode could increase enemy presence, strength, health, and/or techniques, forcing you to adapt or promptly perish.
#3: As many have said, increase the money sinks. Supplies could be found free everywhere (harder difficulty levels could adjust this), and most players probably found themselves spending money only when they needed or were guided to (i.e. Hylian Shield, extra tunic). This means more mini-game ideas and gameplay reasons to refill on supplies. A bank would also be nice, as extra money could be stored there. Perhaps there could be a gladiator-type mode where you take on challenges and bet on your outcome, such as defeating three Stalfos in one minute without taking damage. If you fail to meet your wager, you lose money. If you fulfill it, your money increases. The more battles you win, the more substantial rewards you earn (such as Pieces of Heart or upgraded wallets).
#4: Dungeons that can be redone, possibly with additional challenges like time and heart loss. Majora's Mask had only four major dungeons, but made up for it somewhat by having each one able to be played again. Ocarina of Time could do the same thing and reward you for completing challenges.
But like I said, Ocarina of Time was and still is an incredible game. There are all kinds of ways to refine it, so maybe we can hope for the next Zelda game or another Ocarina of Time remake far down the road to use these things.
Quite a few things really. Some of these have already been said but still...
- HD Graphics
- More Sidequests and things to do outside the main quest
- Don't make items useless after one dungeon or not useful at all
- Increased Difficulty and Hero Mode
- A savage labyrinth type dungeon
- Fix the Rupee System (I cannot count how many rupees I must have waisted in game)
- Better Character Depth (Majora's Mask had tons of it)
- Spread out the story more
- More locations and make Hyrule Field less barren
- Make the controls better (although this was achieved in the 3DS remake)
- Bosses all have at least two phases