I'm only here as a PPL holder, but a couple of things come to mind.
First of all, pilots are not perfect, so we can't expect them never to make a mistake. As with the Turkish 737 at Schiphol, here three professional pilots managed to make the same mistake at the same time...so there must have been a set of circumstances that all added up to give three different people the same erroneous view of the world. And as most pilots probably think in the same way, you can see how that can happen.
In my industry, we had a fatality not so long ago where a highly experienced, highly proficient guy accessed the wrong piece of equipment. No reason could be identified. Procedure had been applied correctly, but it seems he simply suffered a moment of 'brain fade'. Without going into all the details, the HSE gave the company and procedures a clean bill of health. This poor guy had simply got something in his head that was incorrect.
Secondly, what about a GPS connection to the autothrust that would give a config warning (or even intervene) if take-off thrust was applied at a point not agreeing with the FMC departure runway? Surely that couldn't cost too much...