Trying to generalize the election nationwide and drawing lessons is not going to be productive.  

The author did note  Trump capitalized on the wins in regions that mattered whereas Clinton ran up her numbers in places that didn't (NYC, LA), but didn't put enough emphasis that this was the crux of the reason for the outcome.    On a tactical level the fact that Trump spent all his time flying up and down the rust belt and Florida (the so called 13 battleground states) and targeted his advertising in the key states of the Rust Belt meant he had a stronger instinct of what he needed.

Clinton was in Louisiana in the last week of her campaign - her campaign advisors gave her bad advice.

Other indications of serious mistakes came from indications that Bill Clinton was warning her team that they need to talk to the working class in the rust belt.  They laughed at Bill.  

Days before debate 1, Clinton was studying facts, Trump made many stops in the rust belt.  Who did their homework?