Gathering fatigue has its place as many have stated. Since everyone can mine the same mining point there needs to be something to limit the amount of ores/logs that are entering the economy. That are measures in place for battle farming as well. Many mobs have crazy terrible respawn rates which limits the amount of drops one can get. From experience, I've noticed this with toads, ghosts, and bombs; I'm sure it applies to many other monsters as well. Crafting is a bit different though as its zero-sum process. You are using up materials to make materials, so there doesnt need to be any limits in place.
Hopefully that makes sense.
That all being said, I would like to see a more creative method to gathering fatigue. As it stands right now, its very frustrating and some what mysterious as the game doesn't let you know that gathering fatigue exists and that its taking effect.