BIOSHOCK SPOILERS:
The entire game sort of derailed for me after the Ryan event--Cohen's artistic madness would have made for a better foil to Ryan's hyper-rationality. (And, in fact, I thought he was being set up as that--not as a one-off area). Fontaine is--what? A mobster? What's his goal or purpose? For game that prided itself on its narrative and philosophy, the entire last third is pretty much "kill things, you big killer, you." Ryan taunted you for being a slave, a "Parasite," for being ignoble. And because of the nature of FPS gameplay, he was right. That, and the whole "would you kindly?" riff on linear objective-based gameplay, set up a really interesting morality that should have been blown wide open in the final act (ideally with more open level designs and a real gameplay choice about how you choose to deal with Rapture.)
You're also correct that you never felt like a Big Daddy, tragically--just like a guy pretending to be a Big Daddy in a suit. Which doesn't really work. The last boss fight was also totally out of character (wtf), ridiculous, and far easier than any scrap with a Big Daddy in the game.
Other than that, my biggest issue with the game was the lack of any actual significant freedom. There's like, 9 plasmids, and you can carry 6, and 3 of them are useless--why carry Security when you can just shock-n-hack as a free action? (Aside: perhaps hacking was once not a free action.) It bothered me that weapons and plasmids both were on an entirely linear, choice-free upgrade path. I would have liked to have seen some WoW-talent style differentiation in how you choose to "evolve"--maybe even tied to your harvest/rescue choices. Which threatens to drop us into Bioware morality, but would at least give the game some replayability and customizability. It's hard to argue about how it might imbalance the game when shock-n-wrench or shotgun-to-the-face work against every single opponent without fail.
If I sound pissy it's because SS2 is still the better game in many significant ways--freer level design, freer gameplay choices, a greater sense of horror and oppression, and a better narrative arc. Yet despite all this, Bioshock is still way better than Half-Life 2 (imo) and easily one of the best games of the past 5 years. It's hardly a failure--it's just one of the best games I've ever played, instead of the best, like I was hoping for (and, for the first half, felt it might actually be.)
