There would more likely be another prequel set before this one or a setting beyond the time frame of Bio 2 than going back to Rapture. Rapture was chaos when you got there, it collapsed socially (and in many ways structurally), and the Splicers escaped at the end of Bio 2. Talk about irrationally clinging to old ideas, no pun intended.
There's also the fact that this title has outdone Bio 1&2 week one sales figures. You really think they want to go back to the old formula with success like that, esp when story wise it wouldn't even make much sense?