Um... I don't. I compare BG to BG2, IWD 1 to IWD2, Fallout 1 to Fallout 2 to Fallout 3, and NWN1 to NWN2, in terms that each of those games are designed to be related to each other in a series, hence the numerals.
Since Bioshock is not a sequel, to compare it to SS2 as one seems silly to me. Certainly there can be some parrallels, but Bioshock should be treated as a stand alone game without any baggage from previous works.