Well, this is my excellento writing skills (excellento meaning below-average):
Factions:
Brotherhood of Steel after maintaining control of DC, rupture from inside as some Paladins, Knights and Scribes, believe the BoS to be slightly dictatorship-ly as they realise the Lyons bloodline will remain dominant in the leadership. This eventually leads to armed uprisings in the BoS, leading further to full-scale civil war, inciting the Outcasts to join in on the rebellion side of the uprising, DC is divided, as wastelanders stand in awe at the fire power the BoS are throwing at each other.
Talon Company reconcile their forever hostile to certain people ways, by getting a supporting command structure and resort to protecting towns on the caravan routes at low-low prices!!!! Towns such as Megaton and CCommons. They try to stay out of the conflict in DC, but get dragged in as the leaders lust for caps grow. Talon Company fight for both sides, often disappearing from the battlefield when they are about to face their own kin.
Reilly's Ranger takes over a sizeable portion of DC, and open up recruitment posts in most towns, but refuse to operate in towns with Talon Company presence, leading to minor hostility between the two factions. The Rangers eventually become a large military faction with a large amount of land to their name. The rangers refuse also to involve themselves in the BoS Civil War, taking a major hit to their financial state, leading to a state of general displeasure in the rangers' soldiers.
The Outcasts remain in Fort Independence until the battle in the memorial occurred, the outcasts took advantage of the lack of authority in DC and stormed some of the western boroughs, establishing a minor power-base in the capital. When new of the uprising reached outcast ears, the outcasts took advantage once again and attacked several loyalist BoS outposts, and even threatened the Citadel with stolen Tesla Cannon, and other heavy weaponry.
The Regulators continue their "crusade" against injustice, eventually their leader is affected by a severe psychological problem, committing suicide. The regulators without a leader resort to an election of sorts leading to the only candidate to be elected, the Regulators continue to be secluded in their 'justice'.
Settlements:
Megaton would grow due to the increased water in their society. Farms start to grow outside the walls of the city, and smaller suburbans communities develop inside and outside the city, eventually reaching Springvale at it's borders. Springvale starts to burst into life as people move their to be within range of the sprawling city that is Megaton. Megaton develop their own armed forces to patrol and guard the city, but the borders become cumbersome to patrol against raider attacks, so they employ the born again Talon Company to assist in their defense.
Rivet City take advantage of the water purifier location, and start charging tax on the use of water from the purifier (due to the BoS being in turmoil, Rivet City are the only security force left at the purifier), hitting the water caravans significantly. Rivet City, also starts to sprawl, and a small settlement starts to form on the runway of the aircraft carriers, and more people flock to Rivet City, overcrowding most of the decks, eventually leading to sprawling slums forming in the far south-east of the DC ruins. Many battles of the civil war occur in the slums, as the Loyalists and the Rebels/Outcats seek to gain the control and support of the Rivet City populace, although the council of the city prefer to remain neutral in the conflict.
The Citadel is completely changed after the events of Fallout 3. As well as the pentagon, some small slums have formed around the pentagon as wastelanders hear the bravery of the Paladins, and wish to be under the protection of the esteemed BoS. The BoS in the Citadel start to become strained under the weight of all the refugees. When the civil war occurs, the Citadel is severely damaged, and the Outcasts had left their mark on the walls, a gaping hole in the Loyalist defenses. As well as that, some desperate refugees take advantage of the civil war and charge into the breach, a huge amount of wastelanders were hopelessly butchered, at the loss of several paladins. The defense didn't really stem the flow of refugees, and they quickly cork the hole in the defenses with their slums.
That's me done for a bit, god I must've been bored to do that much about the future of a fictional game, but still, wasted time, which is what I wanted. EDIT: I genuinely think the Brotherhood civil war thing probably would've been more interesting/original/exciting than Bethesda's story.