or like yarrr the BoS hates mutants, but nobody says a word about you bringing Strong onboard their airship. or Diamond City hates ghouls but nobody actually cares if you bring Hancock with you
game is chock fucking full of things that you'd think would cause interesting system interactions except that they didn't even try to acknowledge any of them outside of stray lines of dialogue
Oh, so many games have companion-related problems. Most of the time devs just ignore it, which is a shame. Other times they try to account for it, such as disguises or "wait over here" cues. Sometimes they even try to avoid it, like in Mass Effect 2, there were sweeping rewrites to accomodate one of the most unique companions (though overall it still doesn't work well). But overall it's just disappointing.
Thinking about it, and this is probably because it was focused and small, but New Vegas' Dead Money DLC handled companions really well. Very immersive and well-realised, even if they might as well not exist once you leave.
Overall, I think the core issue is that companions aren't really treated as their own persons, but accessories; once they're with you, they have no real mind of their own. A startlingly small amount of games with companions/party members/etc try in any way to have them react to the player, let alone show their own free will. Off the top of my head, Dragon Age: Origins did a great job, even going so far as allowing companions to
permanently leave you depending on your actions and choices. Can't think of much else currently, though.
Except you're not really, especially in the case of FO3&4. You're railroaded into a backstory that is at odds with their game design and you're pretty much railroaded into their non-reactive faction stories with unsatisfying outcomes.
The reason FO threads always end up being about Obsidian, is because people have written off Bethesda. Everyone is well aware that Bethesda totally has the capability to do complex quests, they have the capability to write well. What they don't have is the willingness to make their game work with good RPG mechanics, good quest design and good writing.
Personally I thought that they would give it a go this time, after hearing some of Todd Howard's comments about writing. I shouldn't have believed him.
Designing around the writing is key for it to work. For a long time, I felt that Obsidian was the only one doing this. It's only recently with this explosion of narrative-driven adventure games, and CD Projekt's the Witcher, that other devs have really started to follow in Obsidian's footsteps.
And I love it.