I actually found Lanayru Mining Facility to be the toughest dungeon to figure out, mainly because of all the Timeshift Stone puzzles which were only moderately used outside the dungeon. In second place is the Sky Keep, for it's room rearranging puzzles, and in third is the Sandship, again because of Timeshift Stone puzzles, although I think it was easier to figure out because it has only one Timeshift Stone, whereas the Mining Facility seemingly has one for every other room.