That's why education is VERY IMPORTANT, especially HISTORY.Societies tend to forget parts of history and repeat it to varying degrees. They, like each of us, can't keep everything they've experienced and learned in mind at the same time. If you isolate people in smaller remote colonies, they're a lot more vulnerable to powerful local magnates.
I have no desires for ultra dense Planet Wide Cities, hell I hate living in the cities, I like freedom and open spaces.Need? Nay, want. Coruscant is awesome. As is Trantor. Though, ideally, I'd want something that combines both those and large natural areas in something more spectacular. I don't necessarily see those in the Federation though, not yet. But I mean, where did the Iconians go? The Galaxy is a very big place. Heck, it can hide whole Dysonspheres not far from Federation space for a hundred years.
If you wanted large natural areas, Macross Frontier's Island Colony is awesome.

I'm not a fan of "Social Stratification", we see enough of that in reality.Yeah, but I'm not leaving my home. Even after many do, population growth is a result of success. Of people liking where they're at. Eventually the numbers will climb and we can adjust to maintain Paradise or see new problems arise, like social stratification...and maybe new versions of separate-but-equal reintroduce themselves.
I'd rather try to avoid "Seperate but Equal" in a Star Trek future.
A combination of searching for M-Class Planet & Space Habitats.Also, I mean realistically I wonder how habitable even worlds in the habitable zones might be in space. Would local conditions and lifeforms be poisonous or undigestible to us, and incompatible with what we would introduce alongside it? A bit like Eden in TOS but even there the life looked too much like that on Earth. But I don't think we fund a bunch of Earths out there in between a bunch of Marses and Venuses that we can solve population problems with. I mean it would be a lot less expensive to build the most luxurious, opulent, and expansive space stations you can imagine than colonize planets lightyears away. Look at Spacedock or Yorktown. I think there are a lot of diverse and dazzling large population centers in space.
SpaceDock / YorkTown are more like Military Fortress Cities in space.
Space Colonies are completely different.
Some people still hunt for food in rural areas, wild boar hunting is still a thing. Given the Wild Boars are a environmental pest and there are no bag limits on them due to their over population and destroying the eco system for other animals.I think the learning and hard work change. We don't hunt for food or dig wells for water anymore yet we appreciate a good meal after a long day. But I mean, AI's are coming, and we can either evolve or fail to. Different is not worse.
We can adapt, control, and make sure we don't suffer from similar mistakes as in the past.