Is it not the responsibility of the flight crew member doing the walk around to ensure all the gear pins have been removed?
In most airlines it's a joint responsibility between the pilot and the engineer to ensure the pins are removed before departure. However I would suggest that very few pilots would actually physically pull the pins out as this would (arguably) be a breach of an SoPs that prevent the pins being pulled by other than an engineer when they are actually required to be installed (eg. for maintenance action).
I haven't read the report closely, but I'm sure fatigue would be considered as a factor. It doesn't have to be the middle of the night to be fatigued…...