I for one wish I would have focused on building up no more than 3 settlements. I am level 29 with around 60 hours of playtime and I find myself fast traveling to all 12-13 of my settlements constantly because I need to build beds, assign people to work food, drop some more water pumps, and of course defend from attacks. Also, in order to build all these settlements I ended up splitting my early game resources that I got from scrapping all the original junk in the settlement. This prohibits me from swimming in the deep end of the settlement building pool as most of my settlements are just meeting the basic needs of my 10-20 settlers and I'm constantly running out of wood, steel, oil, gears, and cloth. This would be rectified if I spent more time scavenging and less time traveling between settlements for minor issues.
I think on my second playthrough I might focus heavily on building up Sanctuary Hills, Starlight Drive Inn, and The Castle as my three major settlements and use the rest as simple mutfruit farms for cap farming. Then as I get my resource collection over the hump start building up more settlements. Putting a radio in those three and just sending settlers to the other minor settlements as needed.
So what would you do differently?