The Master Quest version of Ocarina of Time was probably among the first things I learned about on the internet, and I've been hesitant to dispel the two decades or so of intrigue it's held for me by actually playing it. Though I've known for a long time it only substantially alters the game's dungeons (including the Ice Cavern, Gerudo Training Ground, and Ganon's Castle, though understandably not the Gerudo Fortress), and even then only remixes puzzles rather than changing the architecture or layout, it remains arguably the fullest "hard mode" experience in the Zelda series as well as being an alternate version of a game I have largely memorized. Well, I've played it, and it's a novel experiment which largely illustrates what makes for good puzzle and dungeon design and what doesn't.
In a number of cases, puzzles have been merely lengthened rather than "improved": instead of simply stepping on a switch that stays down, you must carry an easily-spotted box through no environmental hazards to hold the switch down, for example. These are the most frustrating changes: they undermine the sense that this is any more difficult than before, and when the steps are more hazardous it feels cheap. Enemies are often increased in number and/or difficulty (Iron Knuckles are frequently encountered), occasionally adding interesting wrinkles to a room's puzzle. I found myself more deeply engaged by the combat than ever before, gaining a new appreciation for Deku nuts and the Biggoron's sword. Somewhat more interestingly, the nature and appearance of switches or torches are often changed: they can be hidden high up, in gaps, or disturbingly replaced by cow heads jutting from the wall (this is just in Jabu-Jabu's belly and I think the logic was crystals sticking out from the wall would look unnatural/synthetic). A lot of Song of Time blocks are added and prove to be universally bad additions, because it's just a matter of arbitrarily guessing how many times and where to play the song to get the outcome you want. Taken together, these make up the bulk of the differences in MQ and they narrowly do more to improve the experience than detract from it.
More interestingly, the placement of the small keys, map, compass, and dungeon item are shifted in placement and order of collection to varying degrees. In the most extreme case, the Water Temple now yields the longshot before even the compass is found. As a result, MQ generally requires more complex spatial reasoning and purposeful backtracking than the original, but with drawbacks. While puzzle box style dungeons (see Game Maker's Toolkit's Boss Keys series) are my personal preference, I think Zelda games are at their best when they're varied in dungeon design between puzzle boxes, gauntlets, and lock-and-key types. The original roster of dungeons was well-balanced in that regard but MQ throws it off, turning most into lock-and-key affairs. You're still thinking about the overall layout and what is needed to progress which is enjoyable, but after several dungeons like this and a high incidence of cheap excuses for increased difficulty, the charm diminishes. There are bright spots, like a Spirit Temple room involving a Moblin (previously exclusive to the Sacred Forest Meadow iirc) and a wholly unique puzzle of playing different songs next to refreshingly-not-obvious symbols to progress. On a dungeon-by-dungeon basis it's largely an improvement for complexity, but kind of worse as an overall game.
As a quick breakdown, I would say the three child dungeons benefit the most dramatically, while the Forest and Shadow Temples and Gerudo Training Ground also are noticeably improved. Ganon's Castle, the Fire and Spirit Temples, and the Ice Cavern are lateral moves, while the Water Temple noticeably suffers. I think, broadly speaking, the more linear dungeons (three child and Shadow Temple) had the most to gain from a remix anyway; their layouts were not taken full advantage of in the original, and become more complex and intricate in MQ. The Water Temple, by contrast, was too tightly designed around its puzzle box structure to be easily reworked; the result is shorter, with several rooms rendered unnecessary by the new order of operations and a much lower sense of accomplishment. I think its best quality is that MQ gets you to stop and look at these dungeons fresh. I made ample use of the first person view, something I rarely do when replaying the original, to suss out slight changes and felt newly engaged by a game that's become overly familiar to me.
On the whole, MQ draws out increased difficulty from toying with your expectations and assumptions more than truly improving or refining its design. This grates when it relies on you shooting a bomb flower to inexplicably make a chest appear for you to hookshot to, but feels refreshing when you realize the game has made it so the Spirit Temple is no longer in two discrete halves across time; adult Link must travel back into the seemingly-completed child half, activate certain things, then return as a child to gain keys, then return again as an adult to finish the dungeon (this would probably have enraged me if I looked it up instead of reasoning it out on my own). In this way, it's less a challenging Zelda game and more an inside joke for Ocarina veterans. Mystery dispelled, play the little jingle.
In a number of cases, puzzles have been merely lengthened rather than "improved": instead of simply stepping on a switch that stays down, you must carry an easily-spotted box through no environmental hazards to hold the switch down, for example. These are the most frustrating changes: they undermine the sense that this is any more difficult than before, and when the steps are more hazardous it feels cheap. Enemies are often increased in number and/or difficulty (Iron Knuckles are frequently encountered), occasionally adding interesting wrinkles to a room's puzzle. I found myself more deeply engaged by the combat than ever before, gaining a new appreciation for Deku nuts and the Biggoron's sword. Somewhat more interestingly, the nature and appearance of switches or torches are often changed: they can be hidden high up, in gaps, or disturbingly replaced by cow heads jutting from the wall (this is just in Jabu-Jabu's belly and I think the logic was crystals sticking out from the wall would look unnatural/synthetic). A lot of Song of Time blocks are added and prove to be universally bad additions, because it's just a matter of arbitrarily guessing how many times and where to play the song to get the outcome you want. Taken together, these make up the bulk of the differences in MQ and they narrowly do more to improve the experience than detract from it.
More interestingly, the placement of the small keys, map, compass, and dungeon item are shifted in placement and order of collection to varying degrees. In the most extreme case, the Water Temple now yields the longshot before even the compass is found. As a result, MQ generally requires more complex spatial reasoning and purposeful backtracking than the original, but with drawbacks. While puzzle box style dungeons (see Game Maker's Toolkit's Boss Keys series) are my personal preference, I think Zelda games are at their best when they're varied in dungeon design between puzzle boxes, gauntlets, and lock-and-key types. The original roster of dungeons was well-balanced in that regard but MQ throws it off, turning most into lock-and-key affairs. You're still thinking about the overall layout and what is needed to progress which is enjoyable, but after several dungeons like this and a high incidence of cheap excuses for increased difficulty, the charm diminishes. There are bright spots, like a Spirit Temple room involving a Moblin (previously exclusive to the Sacred Forest Meadow iirc) and a wholly unique puzzle of playing different songs next to refreshingly-not-obvious symbols to progress. On a dungeon-by-dungeon basis it's largely an improvement for complexity, but kind of worse as an overall game.
As a quick breakdown, I would say the three child dungeons benefit the most dramatically, while the Forest and Shadow Temples and Gerudo Training Ground also are noticeably improved. Ganon's Castle, the Fire and Spirit Temples, and the Ice Cavern are lateral moves, while the Water Temple noticeably suffers. I think, broadly speaking, the more linear dungeons (three child and Shadow Temple) had the most to gain from a remix anyway; their layouts were not taken full advantage of in the original, and become more complex and intricate in MQ. The Water Temple, by contrast, was too tightly designed around its puzzle box structure to be easily reworked; the result is shorter, with several rooms rendered unnecessary by the new order of operations and a much lower sense of accomplishment. I think its best quality is that MQ gets you to stop and look at these dungeons fresh. I made ample use of the first person view, something I rarely do when replaying the original, to suss out slight changes and felt newly engaged by a game that's become overly familiar to me.
On the whole, MQ draws out increased difficulty from toying with your expectations and assumptions more than truly improving or refining its design. This grates when it relies on you shooting a bomb flower to inexplicably make a chest appear for you to hookshot to, but feels refreshing when you realize the game has made it so the Spirit Temple is no longer in two discrete halves across time; adult Link must travel back into the seemingly-completed child half, activate certain things, then return as a child to gain keys, then return again as an adult to finish the dungeon (this would probably have enraged me if I looked it up instead of reasoning it out on my own). In this way, it's less a challenging Zelda game and more an inside joke for Ocarina veterans. Mystery dispelled, play the little jingle.