Majora's is definitely harder than OoT. It takes a certain something. You have to know what you're doing. In OoT, generally, you can just keep going, figuring out each room and moving on. If you're stuck, keep going forward. This strategy fails in the Water Temple, which is why people always have issues with it. I didn't ever really think of it like that until much later; I had trouble, but figured it out and moved on.
In Majora, you need to have a basic plan for your 3 days. Even if you're not really sure of the details, you can't just do whatever whenever. You need to take lots of interconnected events into account as well. It reminds me of the Water Temple, actually. Both have a central area with offshoots in the four cardinal directions. And in both, you need to understand the basic mechanic of the area. One has water levels, the other has time. This is why both are considered more difficult, I believe.
I had to use a strategy guide in MM for only one thing; the All-Night Mask. I knew the basic idea of what it had to be, and a decent idea of how to get it (I already suspected the store). But I didn't know the part about taking out the thief the first night. It's things like this, the intense amount of connections, that make MM such a tricky game.
I think MM is underrated because it's a sequel. OoT was so amazing and revolutionary. It was an impossible act to follow, in many people's eyes. And then, out of nowhere comes Majora. It's such a radical departure from anything else before it. It was the second game to leave Hyrule, LA being the first. Both were sequels to amazing games, and I feel both are forgotten due to their seeming irrelevance to the main story. LA, and MM at first glance, don't concern Hyrule. They're seen as less important.
Also, the people who hated the Water Temple would not like the time mechanic in MM. Others would also find it tedious. Thus, people see a game that does little visually to improve on OoT, is just a sequel with no importance to Hyrule, and has such a bothersome mechanic to playing it. This combination leads people to write it off as inferior.
That was a lot, and kind of rambling, but the points are in there somewhere...
