Ni No Kuni 2 and Nelke & The Legendary Alchemists both have city building elements blended into JRPGs. Nelke is part of the larger Atelier franchise and Ni No Kuni 2 is Ghibli related. Pathfinder Kingmaker has an entire kingdom management layer that I'll be honest I did not get that far into to play with much if at all.
There's Harvest Moon: Light of Hope. It's not a game I've played but had heard good things about. It is however a farming sim and so not sure if it's up your alley specifically. Coral Island also has some of that but it is another farming simulator and so again not sure it'd be your thing.
I also thought of Dark Cloud but it was less city buildery and more like a puzzle when it came to those mechanics? I guess it counts though.
Amazingly enough, there is a Fallout mod for that: Sim Settlements 2 for Fallout 4. It's less of an overhaul of the Settlement system and more of near total conversion complete with its own storyline, characters, and full content patches. In fact yesterday the team released their 3.4 update; Weapons of Mass Destruction, with a trailer during Bethesda's Fallout Day presentation.