Having only played the 3DS remakes of both, I can at least say this: Majora's Mask has aged better. Ocarina was great, but on the whole, there are just some things that hold it back. While I think the main quest is very enjoyable, with great dungeons, it's the sidequests that are really lacking. Now I'm not saying that because they're less elaborate than Majora's are, that's fine with me - it's not the focus of the game. The problem is just how unfun Ocarina is to 100%.
Think about the Skulltulas. While I really like that quest, it's actually really tedious to finish just because of how complicated it is to work out which ones you are missing, and where they are. The map shows you an icon if you found all of them in an area, so if it's missing, you know just where to look. The problem is that, even if I know there's still at least one Skulltula in, say, Death Mountain, I don't know which part of it it's in, wether it's in the future or in the past, where to start looking. This means I might go back to the past suspecting I missed one there, which forces me to go back to the Temple of Time, watch the sword cutscene, and either make my way back up the mountain or use the Bolero of Fire. Didn't find it in the past? Warp to the Temple of Time again, watch the sword cutscene again, go back to Death Mountain once more. Ooh, there it is! Wait, there's still more? Did I miss the soft soil spot? I did miss the soft soil spot, didn't I? Back to the Temple of Time then. Hmmm, gonna have to catch a bug. Warping to Kakariko Graveyard to catch one, then warping to Death Mountain again. That's not it. WHERE IS THAT THING?? Go back to the Temple of Time yet again to look for it in the future. (and so on)
The above is an account of my own experience trying to 100% the game (I gave up when I couldn't get the stupid cow), and it just stopped being fun when it came to do the finishing touches. Time travel is really tedious, so I wanted to avoid doing it as much as I could. The warp points often being out of the way didn't help much either.
I can't really fault the game for that seeing as it's so old, and it DID do a lot of things right. I just think that some of the mechanics are really outdated, and it's noticable.