There are factions with actual bases of operation that have actual goals that kinda, sorta make sense. In Fallout 3, all the factions are retarded and make no sense. Especially side factions and minor settlements. You could argue about the Institute's motivations being kinda stupid, but compare that to FO3 where the central conflict is about who gets to use a water purifier that everyone wants to use, and where there's a city of kids, and a guy in a tower who wants to nuke a city because it ruins his view, etc etc.
The Lamplighters, the vampire cult, and so on were all incredibly ass in Fallout 3. In addition to the vampire cult, the settlement where the quests start didn't make much sense to me. You look around the Bethesda games with the big raised bridges, very few of them are standing. You'd think the people there would have to scrounge around to live, right? You can't really grow food on top of a bridge. So, I would assume they've noticed most of the other bridges collapsed. So, they continue to live up there? Sure, it's easy to defend since it's up high, but you're all dead once that thing falls anyway.
I can't imagine a good explanation for Megaton, honestly. Pretty much everyone that lives there knows exactly what that thing is in the middle of town, yet they built walls around it and moved in anyway. To make matters worse, they know it's leaking radiation, and still live there. So yeah, pretty retarded. I honestly don't think I've ever seen anyone defend this as anything other than a really stupid idea.
Rivet City also makes no sense. Sure, easy to defend, but that thing is still floating in the harbor there. It's not beached or grounded. It's floating. Wait, did I say it's easy to defend? What I mean is that it's easy to defend until someone with a rocket launcher pops a rocket in to the hull near the water line.
Yeah, Fallout 3 had a lot of really bad locations.