Actually the FEV in DC doesn't make sense, the FEV was originally a top secret project conducted in a military facility. The Super Mutants weren't even the original result of the FEV experimentation, the ywere created by further experiments by the Master. The FEV was also stated to be very much localized to the California area, with the Enclave even having to dig up the Military base to retrieve the virus. If it was in some random Vault they would've known about it as they had knowledge of all Vaults. Also there si the question of why did the Vault people even continue experiments after the war and why would Mariposa trust a civilian facility on the other side of the Country with handlind such an experimental virus? It really makes very little sense and with the Super Mutants barely serving any propouse in the plot, having no organization or goals they are also a pointless retcon.
The Brotherhood being there is ok. The brotherhood suddenly becoming White Knights of the round table that spout pseudo Jedi lines like "Steel be with you" tho? No, that's just shitty writting. You are als forced to join them which is just dumb.
And no, the Enclave was very much destroyed on the Oil Rig, they were already a small faction that needed to check their numbers, them suddenly becoming this super army with Vertibirds to spare despite losing their source of Fuel is actually just a huge leap in logic and narrative. They shouldn't have such numbers. And their role in the game was just an exact repeat of their previous plan, that's just lazy writting.
A ghost is whatever. There have always been supernatural elements in Fallout. Alsoyou are comparing a small quest in an early town to entire big plot points of the main game.
The very first quest forces you to kill raiders and a Deathclaw, so no, it's not just low charisma, the game just isn't built to support pacifist routes. Also, just like it happened with FO3, diplomatic options work like Jedi Mind Tricks as they just work on a random chance and many times it isn't even clear why it even worked at all.
It was the same in the originals, it all worked off chance. I agree that I don't like this system anywhere near as much as NV handled it, but simply giving Fallout 3 the shaft for this and not the others is wrong.