Here's my question to the masses here that doesn't seem to have been actually answered so far, WHY was this Pilot denied a clearance through Class D Airspace in this circumstance? And No, I don't think "Workload" in this case is a valid reason and seems to be some kind of coverall being used.
In Aviation we have many safety nets, everyone knows the swiss cheese model, in this case, the Pilot basically bore themselves a hole halfway through the swiss cheese by not being prepared or legal for this flight, there's NOTHING REASONABLE that can be done about this now without a time machine to go back and force them to take the proper steps, there is also very little I think that can be done in the future to stop someone else making similar decisions. What we can do is look at the layer that does currently still exist and focus on making that better in the future. All the talk about a valid AFR and planning IMHO are moot at this point, they've been put out there and should serve as a warning for all Pilots to not take these things likely but the ones reading it are likely the diligent ones that don't need to be told anyway.
Can we focus on the question of why this clearance for what seems to be a few minutes of transition was denied and thusly this last safety net that could have prevented this and other accidents in the future failed? If we can ignore the other parts we can't really fix and focus on this question then we can get to the heart of trying to find solutions for the future.