Yes, good point there about the flying pots. It certainly makes you jump high the first time when you weren't prepared... And for what price?
In Ocarina of Time Master Quest they have actually removed a lot of enemies in certain temple rooms, so you can focus on the puzzle.
Now I am playing Majora's Mask and reacted when I walked around on the peaceful shore at the great bay. Suddenly a lot of "sand spinners" from the
OoT desert pops up. The music is so mystical there, and these sand spinners destroyed the whole "abandoned beach" environment.
It feels like they refuse to have too few enemies out there, and they definitely put them at the wrong places.