I think the second one also being set in Rapture was kind of unnecessary and seemed like a cash-in to me (though I still haven't played it and really need to). But I feel that the choice of having #2 in Rapture created this expectation that Bioshock=Rapture (sure, I found Rapture very atmospheric and awesome, but the relationship between the city and the story are what really made me like the game), but it made gamers think that the whole point of the series was the city and its inhabitants, so it garnered an expectation that all the set pieces had to be there for it to be a Bioshock game. However, if they had gone straight from 1 to Infinite, this Bioshock=Rapture expectation wouldn't have been as strong, and gamers would see it more as a series about tech way ahead of its time and (for lack of a better description) biological weapons and stories centered on the structures of societies.
Sparknotes Version-lovers of the first game are more likely to say "it's Bioshock, but in the sky" because the progression went Rapture->Rapture->Sky instead of Rapture->Sky
Sparknotes Version of Sparknotes Version-I don't think Bioshock 2 was a good idea (but I haven't played it so that's just an outsider's opinion).
Also, I'm thinking that the story will revolve around the idea that the government of Columbia is in some way using Elizabeth to keep the city happy and afloat but, in doing so, causes her great pain and suffering. Therefore, you're sort of faced with the question:"Is it better to let one innocent person suffer so that many more people might be happy, or try to save that person and, in doing so, cause much more suffering than there was before?"
