I love Fallout 3. I think it's an amazing game and it's one of my all-time favorites. I also generally roll my eyes at people who dismiss it and basically lose a lot of my respect for their opinions. BECAUSE I AM AN INTERNET FANBOY AND MY OPINION IS, OF COURSE, CORRECT.
If I was, however, able to write Fallout 3 in the era it was released with all my present-day knowledge and not have to worry about things like data-drives or more then I would make the following changes to the game just as a matter of preference.
Also, I'm assuming the ending is "pre-fixed"
Twelve Changes I would make as the Fallout 3 Developer
1. The Purifier is going to make Washington D.C. Green again: The Purifier isn't going to provide water because like aliens stealing our water, it makes no goddamn sense. Instead, the Purifier is designed to actually remove the radiation of a given area by taking it from the river and gradually decreasing it directly. It's SCIENCE MAGIC basically but it explains why everyone wants the fucking place.
2. New Reno up the DC Ruins: One of the things I hated about F3, the ONLY thing was the absence of a big community where you could do a lot of weird stuff. So, I would add a third underground settlement or maybe expand Underworld into a mixed ghoul/human community which exists in one of the subway areas and have stuff to do there. Gambling, an adventure chain with bad acting in a B-movie plot, and a brothel. I'd also add slaves there so people know who they're buying.
3. Add Crops outside of Megaton and the other settlements: I would also have the option of going on the deck of the Aircraft carrier and discover they've made dozens of boxes there full of crops.
4. Get rid of Harold: I love you Harold but I would prefer an original character to be in your peculiar position.
5. Replace the Enclave with the Sons of Washingron: As much as I love the Enclave, I think it would be more fun to have the Enclave be the descendants of a bunch of United States soldiers and a member of the Enclave who was trapped in Washington D.C. when crap went down. This new but nearly-identical faction would be led by the ZAX computer programmed to imitate him and Colonel Autumn, who was his descendant.
6. Give the Chance to Join the Sons of Washington or finish the quest by siding with Rivet City: Basically, a Good, Bad, and Neutral Karma option. The Sons of Washington would also be more overtly fascist with the idea they could use the Purifier to create state they could conquer others from.
7. Get Rid of Talon Company: Talon Company is replaced by members of the Sons of Washington who are hunting you because you're interfering with their plans. I'd also make it clear via documents that Mister Burke was a spy working for John Henry Eden, who is still a psychopath in this version. They also only hunt you if you thwart some of the SoW's plans.
8. Talking John Henry Eden to Death is difficult: It should have the best writing in the game and make logical sense as you emotionally break the figure.
9. Get Rid of Little Lamplight, Fix Super Mutants: You could savage the concept but it's much better, I think to have it inhabited by Super Mutants. Lamplight City turns out to be a community of Super Mutants which are entirely friendly and are not the ones who are engaged in a war with the Brotherhood of Steel.
The Lamplighters are normal, if Yellow Bulky, citizens who live and trade with other people. The Super Mutants who are fighting the Brotherhood of Steel are a combination of the violent ones of their kind (equivalent to Raiders) as well as those who believe the BOS are trying to commit genocide. If you help them around Lamplight, they'll let you into the Vault to speak to their leader without violence.
10. Gray up the BOS a bit: Since the Pentagon is such a big place and so few adventures, add some fun ones. You should have the option of assassinating Elder Lyons and replacing him with a man who wants to return the BOS to its roots (but who will still fight the Sons of Washington for their tech). There should also be signs Elder Lyons is actually awful at his job and that the war against the Super Mutants was just his murderous racism against nonhumans rather than doing good--so you can persuade him to stop trying to wipe them out or step down for his daughter.
11. Romance Options: You have the option to date a number of the women and men in the game as well as companions.
12. Evergreen Mills is a violence-free Raider Zone: You can go there, shop, talk to the Raiders, and learn their backstories. It turns out that all of the Raiders you've been fighting are the people of Evergreen Mills that got tired of being crapped on by so many other factions. After a famine wiped away their crops, they turned to raiding other settlements and traders to survive and have actually wiped out at least one completely.
If you wipe out Evergreen Mills, even Three Dog goes, "Damn, man, that was cold."