Here are just a few options I thought of:
1) You could start in an "ok" Rapture back when it started, much like how Half Life 1 starts and then you see it all going to sh1t, maybe they tried sending extermination teams down etc. That would be really cool.
2) Jurassic Park 2: The lost world. There is a 2nd Rapture - this would be a lame and easy approach.
I certainly cannot wait though, Bioshock was incredible.