All the dungeons seem to be much better in OoT:MQ. Dodongo's Cavern and the Fire Temple are noticeably more fun. Especially after having played the original version. Many of the puzzles are in the exact same rooms, but they are totally different.
I never tried Master Quest, not entirely sure what the difference was of the game. But Ocarina of Time remains one of my [and probably everyone here's] all time favorite games. I can't justify trying Master Quest right now though since I'm behind on a few Zelda games.