That's TNG thinking. Once Bermaga got ahold of the show they had no understanding of what a crew does, and what it takes to run a massive ship.
While that may be the case, that is what was represented to us in TOS movies and TNG and on.
However, I think you're getting carried away with your dislike for Berman and Braga. Even in our current day and age, automation is becoming a way of life. Functions are diagnosed and managed by computers. Much different than how it used to be. Hell, we will have cars that will be driving themselves hitting the market in 15 years give or take.
What it takes to operate a ship in the 70's is much different than today. And today is much different than what will be in 300 years. You don't think that the responsibilities of the crews on the LCS class ships are vastly different than that of the crew of a battleship in the 18th century?
The idea of the pilot becoming irrelevant(which it already is becoming, compared to only 3 decades ago), is not really a stretch. Nor is a "pilot" being able to select from an array of pre-programmed maneuvers.