I've actually though of something now too.
So, after deactivating the bomb and moving into the town, Simms asks if you want to do another quest. The quest involves going into Springvale and dealing with the raiders, when you got the school, instead of being all hostile, the raiders in the outside would be friendly, also there would be 2 to 3 raiders in front of the main entrance plus their leader, you would have a conversation with him, which would make the quest solveable trough 3 ways. First, you would say something along the lines of "I'm sure we are all tired of talking, let's finish this now." to wich the raider leader would reply "Alright, time you meet end!" , which would make all the raiders hostile, forcing you to kill them all (both inside the building and outside). Then, the second way, by passing a speech check (around 40 speech would give around 60 to 70% of suceding, it would make the raiders stop raiding Megaton and move somewhere else. The third way would be the hardest, you would not only convince the raiders to stop raiding Megaton, but also make them protect it and Springvale (more on it later), but it would require quite the abilities, around 50 to 60 in speech to get the same 60 to 70% chance of sucess.
Springvale would be a bit different. First, in place of some the ruins, a few tents, and also small farms, they wouldn't be enough to feed all of Megaton (which would be a bit bigger than in vanilla FO3) making the caravans nescessary and vital to the town's survival.
Now Megaton. As I alredy said it would be a bit bigger than now (but a metropolis), it would have a small market, a brahmin pen, butcher, a small barracks (maybe the old armory, but a bit bigger).
Now the main quest. Changes will start right at Raven Rock. You won't be able to convince Eden to self-destruct the base, and the auto-destruct code would need voice verification (It would need Autumn's voice directly). but inside of the Colonel's quarters, you would find the Adv. Power Armor MKIII, togheter with a holotape, explaining where the armor would be (Autumn's bodyguards, the Presidential Guard and Sigma Squad Leaders), apart from the one in the room. It would also be the best armor in the game, with a full set in full condition rendering 75 DR.
Then after starting Take it Back! when you get to at least that destroyed radio mast, you will see Horowitzers, they would be responsible for the rockets being fired at Liberty Prime during the battle, also, there would be at least one Sigma Squad at the purifier, the BOS would also send not only the Lyons' Pride to the battle but also a few knights and paladins too.
There will be changes to the last quest in Broken Steel, in the Mobile Crawler at the launch computer you would be able to see how many nukes you had in the satellite, it would display this:
Mini-Nukes 0/4 (fire at Liberty Prime)
Nukes 2/2
You would have the same targets, plus Raven Rock and the satellite itself (though only the Citadel, Adams AFB, RR and self-destruction would be possible), the canon way (would be estabilished in a later game) would be to hit Raven Rock and self-destroy the satellite, them the Sarah's vertibird would taake you to somewhere high and close enough to RR to it get nuked and the satellite debris fall from the sky (Maybe the roof of the Statesman Hotel or other high building in DC?).
I have some more ideas, but I'll write them later.