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I'm playing through Master Quest Quest on the 3DS right now. Having enemies deal double damage (Which is exclusive to the 3DS version) combined with the different, slightly insane dungeon layouts makes me approach the game very differently than any other 3D Zelda. It's amazing.
I think Master Quest is when I started to appreciate Ocarina of Time more. Not that it was better than the original quest per se, but Master Quest was my second playthrough of Ocarina of Time (first was the original quest back when it released on N64) and by then I had gotten over my initial disappointment with OOT and was able to just enjoy it for what it was a bit more.
I found the Master Quest to be much more of a puzzle solving game. I actually enjoyed the dungeons more because I didn't have to worry about stupid enemies ruining my progress. I'm looking at you Wallmasters.