I just finished OOT: Master Quest for the 3DS. I never played Master Quest for GameCube, so I found the challenges in the upgraded temples satisfying. I was fighting myself bloody inside the Spirit Temple; it took me a few days to find all the keys and all the hidden switches. Perfectionist as I am when it comes to games, I wanted to see everything and collect everything. This meant that I explored every little piece of the temples in search of my Golden Skulltulas.
In addition to upgraded temple, all enemies hit twice as hard, which forced me to get good control of Link and learn to avoid attacks instead of just wildly swinging the Master Sword. The double damage made it more reasonably to get up all the Heart-Pieces. Even with all 20 hearts, there are enemies that can kill you in three shots. I recommend that you get the Big Goron Sword as early as you can, I got it right after the Forest Temple (you can get it even earlier).
Another change is that all of Hyrule is mirrored. No big deal you think? I remember thinking that as well, before I started. But as soon as I stepped out of my home in Kokiri Forest, I realized how brilliant it is. Even though I know OOT inside and out, I found myself constantly lost, nothing where where it used to be. I had to learn and explore Hyrule from scratch.
All this made the game feel new and fresh again.