Thankfully the 3DS version has these two things going for them:Bingowings said:
The only thing marring my enjoyment of redoing Ocarina Of Time is knowing There Will Be Water Temple!
*scream*
Eiji Aonuma apologized for the design of the Water Temple in a 2009 interview, and, with the announcement of the Nintendo 3DS remake of Ocarina of Time, specifically mentioned that he plans on changing the gameplay in such a way to make the Water Temple less frustrating, such as making the Iron Boots easier to use.
The Water temple is actually less difficult on Master Quest. The infamous "serpent-shaped" room now has Hookshot targets over the wall, making it easy to simply bunny-hop through the vortex-filled gauntlet.
Side note: I didn't realize that my wife and I were only a few minutes away from the Water Temple before we decided to sell the game (again). I think I would have sold the game anyway had I known that.