I've always thought instincts were a reaction to a situation.
If that's the case, the more you learn, understand, and work on the game the fewer times you have to rely on instinct.
With that in mind, instinct is most relivent at a young age when knoweledge of the game is minimal. As a player becomes more knowelegable the fewer times instinctive reactions occur.
In LL and hs you often hear of players having good instincts, but, very seldom do you hear of a MLB player having good instincts, you more often hear them having a good knowledge of the game.