Classic battle of the N64 titles, suprised this hasn't cropped up yet. I'm not the only agèd one here.
These were my first two Zelda games, so there's a lot of childhood nostalgia clouding about. I couldn't decide on this for years, but now I prefer MM. Here's a breakdown, read it or skip it, so long as you read it.
I know that MM has characters, but I didn't see anything in OoT...
As is probably obvious, people in OoT are just placeholders or cheesy comic pantomine characters. The only exceptions that display any modicum of depth: Mido, Saria and Ganondorf. But really only Ganondorf. I'll give OoT credit for that - to my knowledge, it's the first game where big G stops being the - "bwahaha! Flee my purple pixels of doom!" - animation of the 2D games and becomes the - "My country lay within a vast desert. When the sun rose into the sky, a burning wind punished my lands, searing the world. And when the moon climbed into the dark of night, a frigid gale pierced our homes. No matter when it came, the wind carried the same thing... Death. But the winds that blew across the green fields of Hyrule brought something other than suffering and ruin. I coveted that wind, I suppose." - Ganondorf of actually having something to think about. Still, one proper character isn't a lot to go on.
But in MM, even minor characters often have recognisable personalities or conflicting internal interests. Anju and Kafei, Darmani, Skull Kid, Tatl, various others... all of them have more complexity than 99% of anything in OoT.
MM wins this one like King Leonidas at senior sports day.
This one's tough. For starter's OoT's overworld theme is vastly better than MM. Yes, MM had a decent orchestration of the classic theme, but OoT's overworld theme was new and immersive. It felt like wilderness music, and when it drew to an end it really felt like the end of a summer's evening. But, Clock Town theme was pretty great, and the last few hours in clock town is tres atmospheric. The music for the four regions didn't have anything I could call a tune, but they did give a sinister, wild ambience that was pretty cool. The MM dungeons music, did nothing for me. At all. Remixing the Song Of Time for different effects, was either really inventive or really lazy. I can't quite decide. But other than the Song Of Healing and Oath To Order, I can't remember any of the playable songs on MM. And I found the Deku Palace theme just too catchy! Like, bad catchy when you stop enjoying it and want it to go away.
By contrast, I remember all of the OoT songs. Even a lot of the ambient music still runs through my head - Market Town, Kakariko Village, Spirit Temple (especially Spirit Temple, love that). The musics of the temples are all very atmospheric and appropriate. All in all, this one goes to OoT.
What I didn't like about MM was the regimentally symmetrical overworld. That completely broke the immersion, and for me immersion is a big thing. Like any believable world would have a capital town in a perfectly circular field surrounded by four distinct lands at perfect cardinal points. Bah! Hyrule Field was much more natural, with exits to other areas spread randomly and believably. Being able to trace the water from Zora's Fountain right through to Lake Hylia was a good move. Having said that, nothing in OoT can compete with Clock Town, and once you got to one of the four lands, each one felt sprawling and natural in its own right. Hated Great Bay, but loved the other three, and nothing in OoT could match the creepiness of Ikanna, either.
OoT's world did, however, have a much better sense of history and shared culture. Links between the Gorons, Zora, Impa and the Royal Family (Shadow Temple was intrguiging, speaking of history). The temples of both games were evocative enough. People always forget about the dungeon design, like they're not a real part of the overworld. Anyway, I think MM just tips this one.
MM. No contest. The masks, the bomber's notebook and extensive side-quests, the greater variety of enemies, watching things progress over the three days, the bank and post... that's enough right there, isn't it? Let's be honest, we all got used to the three day thing pretty quickly. Did it REALLY bug anyone past the first section?
The temples might give OoT a fighting chance, because the MM temples were a little lame, but I don't think it's enough to compensate for everything MM gains.
MM had one. OoT rehashed one.
So there we are. That's why MM beats OoT. And let's face it, MM is so much more unique. OoT was a 3D rendering of classic fantasy action-adventuring, MM made an effort to be creatively distinct.