A main storyline that doesn't suck so much. The main story in Fallout 3 is a horrible mess, like in Oblivion you aren't the main character (your father is much more important to the plot than you are). And the whole water purifier thing doesn't make any sense.
More fleshed out locations, Fallout 3 has lots of thing and places but most of them aren't expanded upon or feel unfinished, take for example the Dunwitch Building it ends just when it starts getting really cool.
Better villain, the Master in Fallout 1 was the high-point of the game, before that if you did some side-quests you could gather Info that showed that his plan was ultimately impossible, this caused him to commit suicide. In 3 you convince Eden to kill himself and all his men (essentially convincing him that everything he's been doing for the past 200 years is pointless) merely by saying "but where will it end?".
Darker, Fallout 3 was far too optimistic and happy when compared to the first 2 games.
Better combat, bullets kill people, quickly In Fallout 3 most enemies seem to absorb almost all the bullets I shoot them with. Make ammo much rarer but increase the damage guns do, this means that unarmed and Melee become viable choices and helps with the wasteland atmosphere.
Realistic setting, Nukes fell 200 years ago. 200 years is a long time, people should not still be living in rough shacks, there should not still be medicine in the local supermarkets, Fallout 3 seems to be set maybe 20 years after the nukes fell, there are many places left completely unlooted despite the fact that the economy is based entirely on loot and salvage.
Viable Socio-Economic structure, what do people in the Capitol Wasteland eat? there are no farms anywhere. Certain places like Rivet City have no conceivable way of generating income or trade goods, and no way of getting food from theoretical farms that my exist. How do they survive?