Honestly, the difference between these games is that, OoT feels like an adventure game with an epic quest to save hyrule, MM is more like your MMORPG with more quests then your ever going to do, but more like only 2% of the questing and instead replaces the rest of the 98% with an epic evil faced moon staring down at you 24/7.
Lets look at the major differences between MM and OoT
OoT has:
-Longer questline
MM has:
-Indepth town that doesn't feel like a card board cutout.
-Original development unlike usual Zelda games.
-A little less annoying vershon of your megaphoned fairy.
-A unique magic based on masks
-Intuitive and more challenging dungeons.
I cant think of anything else with OoT because MM does it better. The water dungeon was easily the most complicated dungeon MM had to offer. Most of you seem to think its just 4 dungeons, what about sneaking into the gerudo fortress? What about that dungeon.. oh damn what was its name? you know the dungeon were you get the song were you can make statues of yourself, they may not have been as long as the main dungeons but damn they were still complicated at points. As i remember it there were 8 dungeons in MM all varied in many ways.
As for OoT, the temples were just annoying, i think the forest temple was the hardest to navigate and the water temple was the hardest to remember were the hell you have and have NOT been, and the desert one was just very boring, however i must say that Master Quest variation made the dungeons much more fun and intuitive, a good bit of the time i didn't get how i was supposed to do it all.
The ability to make your sword much better in MM was fantastic(reminded me of a link to the past), they even added a giant sword you could obtain just for kicks as far as i can tell, i used to swing both at the enemy switching between giant bastard sword that must be heavier then Link mode were everything must die in two hits or i`m not killing them properly to shield and sword mode were i deflect every attack and tear everything to pieces when there stunned from a Deku nut.
A bit of a downer in MM though was the stupid final mask you could get that makes the end very easy, and if you combine that with the endless magic milk or just some green potions you destroy the games difficulty entirely, i once tried to win the final boss fight without that mask or upgrading my sword and it was a *****, i died 6 times trying, with the mask and magic i take two hits and its over before it gets fun, although its extremely difficult to get that mask.
OoT had for the most part, better boss fighting, "the end game fight REALLY got me going when the game took my master sword away for a moment" is what i would say if i didn't already prefer the bastard sword.
Also, finding hearts in MM was much harder and lot more enjoyable when you managed to figure out how to get to one after you find the right tool for the job.
EDIT: Oh, and in general i still like both games, its just MM is more to my preferences then OoT.