Bioshock's biggest flaw is that its too hard to deconstruct the story from tapes that are randomly distributed all around the level. They all take place at different times and with different character storylines, so its impossible to piece it all together, unless the kindly goons on GameFAQs write up a plot summary for you. So by the time I got to Andrew Ryan and Frank Fontaine, my head was already swirling from the jigsawed history I knew. The only motivation to continue onto the real bad guy was to seek vengeance for being manipulated. But I didn't know why or what the bigger picture was.
Speaking of Andrew Ryan's death, I hope I wasn't the only one confused as to why he was making me kill him, especially in such a brutal, painful way. I thought after he showed me the truth, he'd have a little more survival instinct. Throughout the game, he seemed like he wanted to live to me. Even as I was bashing his head in with a putter. But go figure an objectivist.
In an interview with Bioshock's creator,
They did address things like the Little Sisters, vending machines, and other things with some Objectivist hand-waving. I still say that no one would tolerate kidnapping or scientific experiments on little girls, but I guess by that point, things were pretty anarchic. One thing that no one addressed was the sharp difference between cultures of Rapture and the civilized world. People have trouble letting go of their old ways. I don't know if Andrew Ryan was that good in his selections, but it was like Rapture became a functioning Objectivist society with a snap of his fingers. Maybe that's why it collapsed.
Overall, I enjoyed Bioshock, and I look forward to playing it again now that I know a bit more about it. Of course, that should have been done on the first playthrough. I'm not sure if it should have won story of the year, but I don't play enough games to make that call.