Not incompetent as such, but do we have to design for the "99 percentile bad" pilot, which may not be far removed from incompetent... Sadly, in many cases this means making the system "less good" than we otherwise could if we didn't need to account for a sub-par pilot.
Another part of the problem is pilots switching between aircraft makes. There is a certain logic to the way Boeing systems work - and it doesn't change all that much between the various Boeing models. Fly Boeings your whole life and it all makes perfect sense. Airbus has a certain logic as well that is pretty consistent between the various model, and it makes sense to the people who have only flown Airbus. But the Boeing logic is different than the Airbus logic. Which one you think is better is largely dependent on which one you 'grew up with', both work, but they are not completely compatible with each other.
It's sort of like driving on the right or on the left - both work, both have people that think their way is better. I grew up driving on the right - it's what comes natural to me. I've driven on the left for many thousands of accident free miles when in other county's (mainly the UK and Australia) - it's takes more attention and is hence more fatiguing - but it's not all that bad so long as things don't go seriously wrong. But I also know and fear that, faced with an emergency situation where I need to take split second action, my instinct will be to 'go right' - which if I'm driving on the left could be the exactly wrong thing to do.
While it has gotten little discussion here, I'm firmly of the belief that Asiana was in no small part due to the pilot transitioning from Airbus to Boeing and that's why the aircraft systems didn't behave the way he expected.