This is a hugely complex issue. Which skills, which aircraft? The human factors side adds to the enormous complexity.
As someone that has worked on and around aircraft for 30 years, been working with airline cockpit avionics every day for the last 15, and a novice pilot with about 350 hours, my imagination literally explodes with possibilities every time the subject comes up.
Of course, skills are forgotten if not exercised. Just migrating from one airplane type to another, even with simple airplanes does that. With small single engine piston aircraft; you start to forget you have rudders migrating from a tail dragger to a tricycle gear aircraft.
In a complex multi engine airliner or a fighter (wildly different universes) there are similarities but hugely more variability.
GA pilots love to point out instances where an airline pilots seems to have forgotten stick and rudder, short field landing and upset recovery skills.
In addition, the human brain likes to assume an activity performed hundreds of times in exactly the same manner will be just like all those previous times to the point the brain may mask an irregularity to the conscious human, when it's observed.
So to some point, even checklists don't work to 10E-19 failure rate, much less sophisticated cockpit automation.
At fault are humans in the loop, which IMO is also fairly presented to the public. Pilots get blamed and are responsible for a lot of the problems.
But, that needs to be put in perspective. Any airplane is a useless pile of materials without a pilot. It is capable of doing nothing, nada, zero that is useful or fun without a human at the controls. The most important system on any airplane is the pilot! It is required for everything to work.
Yes there are some primitive automated flight routines, but it's still at it's infancy.
Humans aren't reliably logical either. Training has a lot to do with it.
I believe we train people to ensure they go through some pre-defined process before they emotionally feel good about taking an action. Academic training alone is not effective.
Humans respond by impulse and emotion. That's why scientists believe in supernatural creatures and bankers live in debt, it's their emotions and impulses runing the show.
I went to an FAA pilot training seminar a couple weeks ago. They show a recording of a pilot safety briefing filmed at American Airlines. I've tried to find a copy to share with coworkers (other Avionics Engineers). It's sometimes called Automation Dependency and the speaker is Warren Vanderberg. Some times it's also called Children of the magenta. It is a real eye opener. I recommend it to everyone in the business.
If anyone knows where to obtain a copy of the video, I'd sure like to get one. In fact, I think I'll call the FISDO and ask today.
I'm not sure how someone distills any subject so complex down to a few root causes. It's certainly an area that is worthy of serious research.