Now I've played all the Fallout games so far, and anyone else that has will probably better understand what I'm talking about here and there. First off is the way F3 was somewhat PG-13'd over it'd predecessors. Granted, I realize you can't get away with as much in a console game as you can in a PC game, especially when the game gets the attention and hype that Fallout 3 has/had. Whereas Fallout 1/2 were a bit more obscure and didn't have the same internet exposure to contend with.
One thing down-scaled from the last Fallout games was prostitution. Greatly. Now I'm not interested in seeing pixelated nipbles, an animated bump n grind, or having a game that moans at me. In the last games you saw people(okay, cut the crap: women) selling themselves all over place. In nearly every town, and in some towns nearly every corner. While it was somewhat amusing to solicit most/all of them, it really helped to get a sense of the desperation in the world and how people were doing any/everything they could to survive, a sense I didn't really get from Fallout 3. F3 has some concern on radiation and it's presence in the world and water sources, but only relatively small handful of people seem to know about it or care.
Another thing, equally naughty, was drug peddling. Now granted, drugs are quite present in F3 and have a reasonable impact on what you do, even allowing you to become addicted(though curiously you don't see any addicts or junkies wandering around ever), but they really seem to more or less come from unseen forces. You never really see any seedy drug dealers, standing around trying to sell you something. Raiders and the like always seem to have some, but dealers, addicts, and sellers of it are MIA. Again, it's not a very big deal. In past games you could sell drugs you found to junkies wandering the streets or buy drugs like Jet from seedy folk all over offering their wares with corny sales pitch lines("Wanna fly?"), and again, it just something that helped you sense the dire situation of the world and how some people were trying so hard to escape reality while others tried their best to profit from it.
Also there is the small issue of slaving. While the system and process for slaving in F3 is pretty decent and works rather well, there isn't the stigma of slaving that came with slaving in the last game, which seems a bit strange. In Fallout 2, you could join in on the trade of selling your fellow man for a quick buck, but doing so made you known as a slaver. And as you can imagine, this made a lot of people a lot less friendly when you talked to them, cutting a number of dialog trees into two line stumps, and in some cases leading to people opening fire on you on sight. Whereas in F3, you gain negative karma, but that's pretty much the end of the repercussions.
Lastly, seeing as I've managed to make a novel out of this post, is children. Or rather the killing of them. I honestly can't see any reason why you should be unable to kill them. Sure, it's an evil thing to do, but so is killing random strangers or selling them as slaves or nuking an entire town. While I can't think of many reasons to go to Little Lamplight and open fire on anything that moves, I'd at least like having the freedom to be able to. In Fallout 2, it was almost fun to do so for the challenge of it, since killing kids made you wanted as a childkiller and would cause random encounters with bounty hunters. There was even a few annoying kids that would harass you so much that killing them seemed justified.
Okay, so that's all I really had. And thank god, because I doubt anyone has the patience to read all that, anyway. Just a few things I'd like to see made more like the originals in future Fallout games. The advlt nature of Fallout was one of the things I liked best about them. Because I'm an advlt, and I like my games to be, too. /end rant