I wouldn't trumpet La-Mulana if I wasn't happy with the overall difficulty level for the most part. There are some outside cases:
Deciphering the doll puzzle is infamous, but then again they use the words TINY DOLL literally in the text pretty plainly so if I'd been keeping pen and paper notes maybe I'd be good? I dunno. I'm OK with only being 95% as wily as La Mulana. That one I figured out but just running around mashing X. You cant throw fastballs and expect anybody to bat it 100%.
The doll was a pffft sound, there was also another one in the Chamber of Birth that involved a very tiny, almost totally invisible picture of a snake that was painted on an already very busy mural wall that I ran past for about 6 hours. Fuck that. For every one of those however there were maybe 10 where I got to do the "nah... they couldn't possibly.... they wouldn't...." and then have the little bleeepibtyblee noise of success indicate that they would. In those moments you feel like a genius. The final puzzle - or set of puzzles - Jesus Christ.
One of the things the devs mentioned is that they wanted to have less situations where you pull a lever and you know it did SOMETHING, SOMEWHERE but there's absolutely no indication of where. I think that's fair. A few times in this game that happens and you're just left scratching your head. You can't continue unless you run around bumping into everything. Even a "something changed in the Chamber of Illusion" would be fine. Solving mysteries is cool, but you can take it to Simon's Quest levels of obscurity.