OOT original is my favourite zelda game, but Master Quest would not be up there with it for me. MQ was enjoyable enough, but many of the dungeons had excessive use of those song of time blocks, which annoyed me a lot. Some difficult parts of the dungeons were difficult because they were ridiculous, like some tiny switch hidden somewhere in which you have to be meticulously observant, with no clues at all. Too much use of din's fire too, constantly draining one's magic. I find the original OOT an absolute breeze, but I found the MC way harder. I still dealt ok with it, but yes, definitely harder.
Rundown of MQ dungeons:
Deku Tree - MUCH harder. Though still not that difficult, but felt more like a proper dungeon than the ridiculously easy original.
Dodongo's Cavern - Much harder.
Jabu Jabu's Belly - Maybe slightly harder? Weird anyway, with the cows.,.
Forest Temole - Much harder.
Fire Temple - Much harder.
Ice Cavern - No difference in diffiulty, but it's just a mini-dungeon...
Water Temple - I disagree with the above poster on this - I found this water temple much harder! But then I never had any issues with the original so...
Well - No difference in difficulty for me.
Shadow Temple - The only regular dungeon in the game where I didn't notice much difference in difficulty. As a result, definitely the easiest of the 5 sage temples in MQ.
Gerudo Training Ground - MUCH harder.
Spirit Temple - SO MUCH HARDER.
Ganon's Castle - MUCH HARDER.
Overall, not too difficult, but definitely moreso than the original. But as I said, most of these difficulties were for silly reasons.
That's for the original MQ. So for the 3DS MQ, also add double damage and mirrored world, making the difficulty gap even bigger.
So for MQ, overall I enjoyed it, but I was really not a fan of the song of time block stuff. Too excessive and you had to stand in the EXACT right spot at times. There was a room in the Spirit Temple which had a particularly awful song of time block puzzle. Some challenges can be fun, but challenges where you have to play the song of time over and over again at the right exact position, full of tedious trial and error, is not fun. Having said all this though, the increased difficulty of the dungeons made them longer and kind of felt more epic because of it.