I heavily prefer OoT and not because of MM's time mechanics.
- OoT had a wonderful world filled with multiple memorable area's to visit, all giving off a different feeling, making you want to come back to these places, especially to see their state after 7 years of tyranny. The feeling of dread having engulfed all of the area's once full of life and joy was amazing to witness.
MM has its memorable area's, but aside from the main area you start in, none of these places are memorable. I can't even remember the names of most area's, while I could draw a complete map of OoT with relative ease.
- OoT has a wonderful soundtrack. From the ocarina tunes to the menacing music as you climb up the stairs of Ganon's castle, everything fits perfectly and nearly everything is unforgettable. MM has such masterpieces as well, but while its OST is larger in size and diversity, it is generally lower in quality. Most ocarina tunes are bland and most area songs are forgettable.
- OoT has fun bosses. They are a bit on the easy side, but all of them are fun to battle against. Finding Gohma for the first time, coming across phantom ganon and even battling the king of evil, all of these were very well done. MM has a collection of mostly the worst bosses in Zelda history. The first boss was laughable, the second couldn't hit you if you stayed where you are and shot arrows, the third boss is irritating due to the swimming mechanics sucking and Majora himself was the second-biggest anti-climax I've seen in a zelda game (first being the imprisoned).
- The dungeons in OoT, aside from the water temple (to an extent), were fun. Places such as the Forest Temple, due to their excellent puzzles, haunting atmosphere and unbelievable melody will never leave my mind for the rest of my life. MM's dungeons were generally mediocre. Not bad as TP or especially PH, but simply nothing special.
I could go on for hours, but I'll just stop here. MM is superior in the sidequest department, but just a little. Also, the three (fourth being limited to a single are) masks were awesome as well, but not enough to put it in first place.
Don't get me wrong, MM is an awesome game and one of the best Zelda's of all time. OoT however is a masterpiece and set the bar for the rest of the series in terms of quality. MM is just different and different doesn't automatically make it better. People talk about MM being darker as well, but darker doesn't mean better either.
Seriously though, Majora was a hilarious boss fight. I can't believe what they were thinking when they made that.