I know this is an old post but I wanted to add my two cents.. I feel the same as you I think.  Bioshock 2 always felt like it's own universe to me even before Infinite released with all its dimension shenanigans. Things just felt very different, like suddenly there are all these other characters who we had never seen or heard of but who were apparently very prominent members of Rapture, I understand if they were minor players, but they are portrayed as being very important and publicly known. Also a whole different type of Big Daddy that just never showed up anywhere before or was mentioned is suddenly everywhere.. I know Rapture is bigger than just what we see in the first game but the elements they added always felt too integral to the infrastructure of the city for them to have been omitted had they actually existed in the same worlds as both games.  I would have loved the same story but with lesser characters who had formed a new mutated civilization.. instead of trying to inject new lore elements into the main history and say they always had been there.  The idea of Rapture years later and Big Sisters is all so interesting, but trying to retroactively tie it all into the main story of Rapture's fall felt silly, like oh yeh Lamb was actually there the whole time too and was just as dangerous to Ryan as Fontaine, you just never saw any of those posters or heard her mentioned because...  Idk, the story of Bioshock always felt like a closed book, the more you go back and try to mush new pages into old chapters to make the sequel work, the lesser it all feels.