Megaton has a live atom bomb in the center of town and a strange man who solicits you to set it off. Arefu has a "vampire" problem and many of the townspeople are dead. The Republic of Dave is ruled by a misogynistic, self-centered, self-appointed despot. Little Lamplight kicks out members that become adults, dooming them to the wastes. Underworld faces constant discrimination and murderous indifference from the BoS. Big Town lives under the constant fear of Super Mutant attacks and kidnappings. Paradise Falls is a slaver town with child slaves in the pen. Finally, Oasis is full of nut jobs who worship Harold and misinterpret his words to forward their crazy agenda. I actually find that most settlements have something dark going on.
Other than that, I very much agree.
Not trying to argue here (sometimes people get mistaken when I type stuff like this), just trying to explain why I don't see much "darkness" in those examples, based on what the game tells and shows us (just offering my point of view):
Megaton has a bomb because people build the damn town around it on their own free will. They knew it could go off at any time and still choose to make the town there. I don't see anything dark in that, only stupidity.
Arefu doesn't have a vampire problem. The Family staged the "attack" so they could smuggle Ian West out of the town unnoticed. So they could teach Ian to control his hunger for human flesh.
Their "vampire problem" is no problem at all, it is actually the Family being nice and saving Ian West by teaching him how to control himself. Also only Ian's parents are dead and they were killed by Ian, not anyone from the Family. One of the Family's members did kill the Brahmin, but the leader of the family didn't approve of this and is really mad about it.
This problem is actually people being nice and helping eachother, that is why the player can just explain what happened to the people of Arefu and can broke an agreement that would benefit both Arefu and the Family via mutual assistance, because both Arefu and the Family are "good" guys.
Republic of Dave is ruled by a democratic elected President. There is nothing showing he is misogynistic or a despot. He has two wives, but treat them both well enough that both are happy living there and not only are happy but one is really in awe and love with him. He is also not a despot since he is not violent and doesn't hold his presidency by the means of using his power to oppress. People are actually happy with his presidency and accept it willingly and without complaints.
We know he is not self-apointed either. This is shown to be false in case the player tampers with the election and Dave loses. He doesn't enforce his presidency by use of force or violence, he actually resigns himself that he lost and that he is not the president anymore. He then leaves to found another settlement. As a note, he even mentions that it used to be a Kingdom (Kingdom of Tom), but he is nicer than that, so he allows free, democratic elections. He could still be king if he was such a despot.
Little Lamplight kids kicks adults so they move to Big Town (and not to die in the wastes) and they also believe big Town is this really awesome place where adults party all day and live a fulfilling and fun "big life". None of the kids believe that they will die in the wastes once they leave Little Lamplight.
Underworld doesn't have any problems with the BoS, BoS do not go to Underworld. The residents even say they live there because no one bothers them there. And some have been living there since the bombs fell. Ghouls have a problem with the BoS because it shoots ghouls at sight, they don't differentiate from feral or normal ghouls. But the BoS does not go to Underworld to kill or annoy ghouls and they don't actively go around looking for and murdering ghouls either, they only shoot ghouls that go near the BoS patrols or their bases.
Big Town is the only settlement with real "big" problems in the capital wasteland (like I mentioned in my previous post). But they could realistically move.
They say they can't move because they wouldn't survive in the wastes. Although this seems very silly because they manage to survive the trip from Little Lamplight, which is in a quite wild and dangerous area of the map. They could also move to Arefu since it is only two "map squares" away from Big Town (it is really close, from Little Lamplight to Big Town one needs to travel seven "map squares"), they could also just go straight to Arefu instead of Big Town, Arefu is on the way of Big Town from Little Lamplight (six "map squares").
Megaton is 4-5 "map squares" from Big Town, so it's not that far either.
Anyway... I got derailed. Big Town is the only settlement with actual serious problems in FO3.
Paradise Falls is a slaver town with kids in the pens. It is supposed to be dark. But nowhere does it show that those kids (or any other slave) are mistreated. Yes, being in a pen and lose your freedom is really bad, don't get me wrong, but for slaves they seem to be very well treated, which makes it a bit less dark.
But what makes it actually lose quite a bit of it's "darkness" is when one realizes that no one else in the capital wasteland has slaves. No settlement have slaves working and no character besides Eulogy Jones has slave servants (not even Tenpenny Tower, where it would make a lot of sense to have slaves serving the rich snobs). The game could have pulled the darker side of slaves if it showed how some "owners" horribly treat their slaves, how slavery and slaves are a commodity in the Capital Wasteland and nothing more than objects or possessions, etc.
About Oasis. Sometimes the well-being of the many takes precedence over the well being on the individual. Even Harold agrees with this if you decide to keep him alive:
Harold, finding a new reason to live, replies that he was selfish to want to kill himself, and then asks Bob if he agrees. Harold finally says that he is at peace with himself and, for the first time in a long time, Harold is finally happy.
So in the end this darkness is actually the "light" and most positive solution. The one that benefits everyone, including Harold. Instead of one (or two depending on the point of view) living being losing his life uselessly and stopping helping the capital wasteland to have more natural flora and fauna (we can hear birds chirp in Oasis).