User blog comment:Pawn of Atlas/Important Discussion for Rapture Storyline page/@comment-189.143.46.245-20140329144427/@comment-867628-20140329145944

The problem with that (despite it being a good explanation) is that Andrew Ryan is clearly well aware of Suchong still being alive, as he says "Yi Suchong is my employee; it was not a deal he was authorized to make", when referring to Elizabeth's deal with Suchong. Also, I doubt Suchong knew Fontaine was still alive; in both Bioshock 1 and Burial at Sea he makes no secret of his loyalty to himself alone (and money), as revealed in his Audio Diaries where he talks about changing employers. That's why Fontaine was after him in BaS, because Suchong still had his "Ace" but was now working for Ryan. The last thing Fontaine needed was for Ryan to find out about Jack before Fontaine could bring him to Rapture.

Unfortunately, Levine may very well have overlooked Gil Alexander here; it's a point many have brought up, that there's definitely an inconsistency between Suchong's death and Alexander working on the Big Daddies. The only explanation I can think of that makes sense is that the Alpha Series were only/primarily present during the Rapture Civil War, but this is highly unlikely, as well as contradicted by the fact that Delta is seen in the intro to Bioshock 2 at the Kashmir on New Year's Eve.