If I wanted to give you a challenge, I could hand you an a N64 and a copy of Goldeneye. "Here, kill all the bad people with your fists instead of guns." Just because something is challenging doesn't make it fun or good. Illogical puzzles (or, perhaps going out on a limb here, "stupid" puzzles that aren't based on logic but pure "piss you off and make you frustrated for the point of defeating you") are not good for adventure games.
I personally hated the puzzle with the clam and the bubble, but it was at least logical. After I solved it by accident, I understood it. Things like having to comb through a library of books to find something was kinda dumb. But there's a happy medium.
It's OK to eat fish - they don't have any feelings.