Let's see what we have so far:
Bioshock - Set in 1960, where a human uses both weapons and plasmids to fight psychotic splicers and two groups of corrupted objectivists.
Bioshock 2 - Set in 1968, where an Alpha Series Big Daddy dual-weilds weapons and plasmids against stronger splicers (Jack wouldn't stand a chance according to the devs), most led by a corrupted altruist.
I'm thinking of where Dr Brigid Tenenbaum went after she left Subject Delta with Augustus Sinclair, perhaps she is fighting with others she brought along (or thiose who followed her to Rapture), perhaps it is a team based combat scenario, Rapture in 1968 is too dangerous for one individual (even with plasmids), but the devs didn't think about a group, perhaps allowing that group to visit Athena's Glory (an area advertised in Bioshock), sort of like Left 4 Dead, but with Bioshock elements as well. Being in a team would also requires commands and also setup combo attacks (e.g. Fire and Ice to crate a jet of water and then Electricity to provide a more powerful shock). Then there's also the fate of Grace Holloway and Stanley Poole...