I think the Nipperkin bit was just to sell MI's 'purpose' (and pirate rule, later revisited in Pirate God) again to new gamers. It has been 10 years, you know. I think that is the main reason.
For the coupon puzzle, it's been a while, but isn't the coupon found in "the wild" useless except for comedy. The really useful ones are hidden away and need to be found (think: Singing fish).
Personally I think the worst puzzle is the opposite Feast of the Senses in Epidose V (however, it's still my most favorite of the 5 episodes). Too fast after the feast, you already have 1/2 the items (if not more) by the time you get the puzzle. It just felt... unnecessary.