I no longer fly Boeings but when I did there was a philosophy mostly ignored by operators that only critical (killer) items were included on the checklist. For example the Boeing takeoff checklist for the B744 was "Flaps ... Set". Everything else (Call the cabin, set the transponder etc) were procedures and did not show on the checklist. This made the checklist effective and more relevant and would, if this philosophy was to be adopted, more likely to be used and to be used correctly.
When the carriers pad the checklists with all the procedural items it is more likely that single items will be missed, and that item could well be the killer item that the checklist was originally intended to protect.
So one of the causes of this accident must be that the crew did not check the flap, or if they did, they did not do it in accordance with the checklist ("Set" would be defined as lever position, indications and lights). Why did they not do so? Were they distracted? Were they used to only paying lip service to the checklist? Had the checklist been padded with extraneous items so that it was really a mini-operations manual?