I'd say they're both stronger in different sets. OoT is hailed as genius largely because of it's time. It really pushed the envelop for what we should expect from a 3D adventure game. The combat was satisfying, the lore deep, the story involved and the gameplay long, with a good mix of sidequest. I'd say the part it excels in is it's narrative. While MM doesn't slack in the area either, I still remeber the feeling of playing through the first game, the mix of action and exploration, the downtime, the puzzles that made you feel clever to figureo out.
MM excelled in that it improved the sidequests, particularly with the mask system, and that it was daring, the timelimit and the transformations both involved mechanics that really excelled and made gameplay exciting. Plus, the masks almost all have involved sidequests, which is oh so satisfying for the completionisits, especially since, unlike games like Assassin's creed and such these days, the collectibles had an ingame impact, and infact the ending changes if you manage to collect every single mask and beat the game.
Personally, I love them both so much. I don't think I could pick a favourite. They both fill different niches to me.
On the note of time limits, I hate them too, but I found that MM did it great. I thought I'd hate it, but it's often more than enough time before you need to reset that I found myself fastforwarding time a lot to get to where I needed to be.