Um. Covenant has major problems and MAJOR TENSIONS and MAJOR HATE for a main faction...?
Their deeper story can also seal or deeply damage relationships with some of the best loved companions if you have one with you. It's not a lot of story but it is a very gray area and for some players a hard choice to make.
Bunker Hill is deeply connected via factions & major storyline, has a very cool reward after a cool storyline, has a cool radiant, has another potential quest which relates to Covenant, can become a settlement only after a certain point in the game, and is connected in ways through the Commonwealth that you only find out through research and has unique and immersive dialog going on when you visit with companions. Let's not forget the traders. It's perfect for what it is - very cool and fulfilling and successful version of a "small town in the post-apocalypse".
Vault 81 is both funny in terms of canon and lore and weird and you can be permanently damaged and one of the favorite characters comes from there - so a fair bit happens. I felt it was a bit light because of the bugged storylines, it's my least favorite overall, I'd take GreyGardens and The Slog as better characters overall even though they aren't fitting into what you consider "towns".
I'm not saying you're wrong but just trying to point out another point of view on many of these spaces.
Atom Cats Garage & Railroad HQ also have some great characters and some specific quests that offer unique rewards as well as some lore deepening in the commonwealth. They're small by the nature of their location and surrounding factors, I thought they were well put together. I'd love more from Atom Cats but they also were very good just the way they are- room to grow if they want to add more to them, but just kind of a fun surprise too.
There is some real disconnection in some of these situations, definitely, but it isn't light on options. Sounds like they just didn't thrill you that much. And that's cool.
In general the dialog trees were small across the board. There were a lot of little uests that were just too easy/linear. This is probably me, overvaluing those things that felt just slightly less linear - I had my disappointment phase in December and these days I'm back to really being surprised at how much I keep finding and enjoying, so grain of salt!
Just wanted to point out a few things in case you missed them.
OH if you haven't yet, try doing all the little job quests for people like the various Drug Dealers and Moe. It's not that the quests are so great but there's some good dialog and just character things that are funny. Or stories like Confidence Man & if you haven't stumbled into the Cannery or a settler with a bad stomach, that's a very good side story as well.