Oh shit, also! I forgot the DLC. Far Harbor was not perfect by any means, but the writing was, again, shockingly good for Bethesda. Having to juggle the three factions, especially knowing what Arcadia had done in the past, was really interesting. And the fact that they raise the idea that the PC could be a Synth because they don't remember anything before the start of the game became my new headcanon, it was such a good piece of meta writing.

I should say though, my one time through Far Harbor I didn't realize that you're apparently supposed to bring Nick Valentine with you, so I might have missed some stuff.