I agree with you on that puzzle in Crystal Skull. You obviously knew it was some sort of puzzle when you got all of the squares as you picked up an object. But you are right...there was no feedback in the game as to why you would do this...how you would use the sneezing powder, etc. "This will come in handy" when the powder was picked up was wayyyyyy too subtle!
Once you realized that the objects could work together in a chain reaction...it was great! A really neat puzzle!
But unless the object was in the correct spot...you had no idea what it did. I accidentally got the record player to play...but hadn't a clue why. And I inflated the balloon...but my first instinct was to put the sneezing powder above it so it would spill when the balloon inflated. Was there a hint or a clue that I missed????