I think something that could be pointed out was that Fallout 3's main quest
technically did have a evil option and its alluded to in the game manual. If you are a good character, yes, you could try to find your dad and help with project purity. The evil opition?
Don't, walk away, never even visit three dog, or just play through it until you think its a good time to say "Thats it im done, I don't give a crap anymore, you brotherhood goody-goodies figure it out yourselves!" The main quest is
optional and its quite feasble to play through Fallout 3 thoroughly and never even find dad (something that is stated as being an option in the vault dwellers survival guide). For one of my characters I
only was a slaver, and I had a blast and felt satisfied when I was done.
This is not to say though that the main quest could not be improved (opition to join the Enclave e.t.c), but there actually is a evil path to the questline: ignoring it, let the wasteland rot. Sure you don't get an "end slide" cutscene but then do you really need that to tell you you're done with the game? You should decide when you're done.