For me, I'd have to say Old School X-COM (UFO Defense, TFTD, X-COM Apocalypse to an extent). I love them in a way that I just do not enjoy NewCOM, but the interface was quite possibly based on the recovered works of a 13th century scribe, and is very difficult to get used to for an unfamiliar player.
Definitely agree with OoT, loved it, but it confused the crap out of me as a kid. I had no clue what I was doing after getting the master sword.
I remember absolutely HATING the water temple until I got a little older. After that it was like "oh...yeah, yeah, raising and loweing water levels, I get it"