I've mostly skimmed most of this post - forgive if this has been brought up before and I missed it (and if it has, then I agree with those who already put it forward, obviously...)
A lot of what gets brought up when people want "mature" content is really just a 13-yr-old boy's definition of the word - or at least is usually implemented in that manner when it gets into the game. Boobs, swearing, and gratuitous violence for no reason, basically. By those terms, most of Fallout 1 and 2 were "mature," but only in those sort of surface aspects. I mean, adding in more six, junkies and such - doesn't really make it all that more mature, I think.
What I'd like to see in a more "grown-up" vision of future Fallout games certainly includes a lot of that stuff, of course. But I'd be primarily concerned with dealing with advlt situations and moral dilemmas. (Actually, I think the Pitt DLC was kind of a good example of that - no matter what you did, you didn't come out of that mission feeling very good about yourself, I think. Actually, I sided with might actually be considered the "evil" side, just because I didn't agree with the methods the "good" side was employing. And this was with my "good" character.)
Most games that have this popular option to be a good guy or a bad guy only deal with black and white definitions of that. You're either the most evil guy who ever walked the earth; or you're a goody two-shoes. Being "neutral" usually means just being very schizophrenic and drifting back and forth between acts of ultimate evil and pure goodness.
The really evil people in the world (and in a well-written story) don't think they're bad guys. The worst of the worst actually feel that they're acting for the better good, or at least have compelling arguments for their actions. (Actually, to give credit where it's due - I honestly thought "President Eden" gave some very good rationalizations for his master plan.) The eviller a villain is, the more convinced he is that what he's doing is actually the right thing. The most compelling of all actually leave you wondering if maybe he wasn't in the right after all. Sure, there's just plain mean people in the world - but that's often a pretty two-dimensional character; and I don't think it makes for a very compelling protagonist.
Conversely, I'd imagine it's pretty hard to be "good" in a world like Fallout. I mean, look at the Mad Max movies - Max is pretty much the epitome of a reluctant anti-hero; and he's just about the most moral person you find in all of the movies. I don't think good deeds should be the default action when faced with a dilemma, with "evil" being the alternate path. I'd rather see it being a challenge to be the good guy all the time. Just what is your character's own moral compass, and what is he willing to sacrifice to stay true to his ideals? All those beggars you come across in Fallout 3, for example - giving them some purified water nets you some good karma. But it's really not costing you much of anything. Pure water is somewhat rare, but it's not all that hard to come by, and you're hardly handicapping yourself even if you give up your last bottle to him.
If a moral decision like "should I help this guy out," doesn't make you pause and think for a moment, then I can't really qualify it as a "mature" addition. It shouldn't be about
whether you're good or evil, but in
how good or evil you are. Take the fate of Megaton, for example. As it stands, it just comes down to "is my character going to be good or evil." Even if the "evil" option means killing tons of people - it's really not very mature. Because it's a pretty simple decision when you get down to it - most people know ahead of time if their character is going to be the good guy or the bad guy, so you just pick which one you want - I'd guess most people knew at the start of the game which they were going to do.
But if there was actually a compelling reason why Megaton should be blown up, then that would have at least helped to make it more mature. A couple hundred caps isn't going to buy you much - what if the reward was a couple thousand, even? Or if detonating the bomb might have actually done some good (don't know what that could possibly be, but it'd be possible.) If the offer was compelling enough, it might have been hard for even a "good" character to turn down.
Anyway, those are my thoughts.