Still, you're not going to know the location of them all the first time you play, so I still don't see how you can say it doesn't count. Sure, maybe after the fifth time you play it you might have it memorized, but I always assumed we're talking about the first time we play through said game and...
Uhh, well..... do you just look to a walk-through for all of those side quests? Because you pretty much contradicted yourself right there. I think hunting down poes in TP took much longer than anything that MM had to offer when getting 100%, and you can't say "unless you count poes" because poes...
Yes, it definitely would've benefited from more dungeons. Of course, it's still a good game, but I'm not the type of person that likes to spend the whole game doing mostly side-quests because there was a lack of main dungeons in the story. But, I don't think the goal of Majora's Mask was to...