Yeah, there are some plot holes mentioned here are really bothering me and I'd love to hear more analysis and explanation of them. Specifically, how does the climax of Episode One even occur (granted, I'm hazy on the details) if it's pretty definitively established that at that point in Rapture's history, Big Daddies are ambivalent toward Little Sisters? Furthermore, how does Elizabeth (be it an Elizabeth or the Elizabeth -- this is a larger, and more frustrating, challenge) dying at the hands of that Big Daddy result in a mortal Elizabeth spontaneously appearing at the exact same site?
Another question I'm not seeing discussed is how Elizabeth could possibly prognosticate Sally's rescue at the hands of Jack. Sally is with Fontaine, who's clearly about to go on an ADAM bender; why on Earth would he not just split the girl open right then and there and harvest her? I can understand the moral victory of knowing Jack will save the rest of the Little Sisters lucky enough to be under the protection of Tenenbaum or quickly bond to a Big Daddy before being found by Splicers, but knowing that Sally will be saved specifically? I don't see how it's possible, bearing in mind that it's implied we're literally watching the bonding process spread throughout Rapture in real time, unless I've misinterpreted.