What you say is true, but I would still disagree with the overall assessment. To put it bluntly, it is the pilot's job to be thrown into unexpected situations. Modern airliners mostly fly themselves, and the pilots are there to a) coordinate with ATC b) step in when the shit hits the fan, which does happen with some regularity. Ultimately this accident was caused by a confluence of many factors, as is often the case, but my read on the situation is that a competent pilot should have been able to handle this emergency without any losses.
Modern commercial aviation is extremely safe because of investigators and regulators banning this "well the pilot just fucked up" explanation and instead looking at systemic factors.
As pointed out in the article, if the pilot was so incompetent, why didn't they receive further training, or if truly untrainable, fired? The airline and regulator have the responsibility for doing so, and ending the investigation at "pilot error" guarantees that another incompetent pilot will crash another plane.
Sure, but if the pilot isn't trained appropriately and has no negative feedback on his skills, how does that situation resolve itself? It's not like the pilot can just take the plane out himself for some practice in normal mode.
It reminds me of the parable of the junior developer who wipes the production database: one person may have pushed the button, but a lot of things had to go wrong to get there
Looking back, much of pilot training is handling things gone wrong and honing skills that keep things safe. CFI would make the joke we were going to practice crashing, as almost every flight would lose a (simulated) instrument, engine, or have something abnormal happen.
Looking at my training, I had about 7-8 hours of dual training - landing, takeoff, radio/tower, spins/stalls (w00t) - before I flew solo. From there, my world slowly expanded to not getting lost, staying out of clouds, and other more advanced topics and areas further from home. Suspect it was another 40'ish hours of learning about crashing. :)
FBW with servo delay, manual trim that you do not use often etc. would be a severe problem in a situation like this, especially for a guy who was captain on an IL-76 (where the yoke is the size of a cab truck steering wheel and has direct feedback from actuators). He "should have been able". Also AFL "should have" provided training in direct mode flying. The OAK "should have" provided an SOP for resetting the flight control computers into normal mode, or some kind of alternate mode which at least would provide auto-trim. Etc. etc. etc.
It is very tempting to say "pilot error" but if you drive a car and the way the steering wheel responds to your input drastically changes in an instant, without you having experienced that way of the steering wheel reacting - is it your "error"?