So I went back to playing Bioshock a couple of days ago, and I must say, if I knew the horror aspect was going to fizzle out so soon, I'd of probably finished it two years ago.
The main disappointment of Bioshock was it's lack of variation; enemies were placed into the game far too often, the game would have been far more intense with less enemies.
Too much ammo was readily available is another reason I can feel this happened, where it got to the point that I was literally running into rooms killing splicers with no apprehension, because there was no need to fear them with such an arsenal in my hands,
There were certain aspects of the game that kept the experience fresh, throwing in the Houdini splicers, along with the 192 serum screwing up your plasmids, which I found entertaining.
Another good portion of the game was Sander Cohen's level, slotted in as the one section of the game where it was not a requirement to kill a boss, giving you the choice instead to just let him live, his level also put quite a nice spin on the game, taking photos of the people who had betrayed him once you'd killed them.
I did quite like the death of Ryan, and the 'Would you kindly' segment did play well, if not a bit cliche-movie-twist, but the whole idea of mind control with the phrase had been used to a nice effect, but to be honest I couldn't stand Fontaine, his voice was far too annoying, and as a final boss he was slightly disappointing.
Becoming the big daddy was lacking somewhat, and should have been slower, but again, it was a nice variation.
The end was definitely lacking, not sure what I was expecting, but it was not it. While it was half decent, I'd of liked to have known what had happened to everything else, such as Rapture itself.
I appreciate what 2K were doing when they made Bioshock, they pushed the boundaries on the appreciation of asthetics that FPS seem to lack, but too many ideas were put into the pot, and made for a disappointing game that was perhaps regarded a bit too highly.
I've recently played Bioshock, and I find I must disagree with almost every point you raise here. When I finished it I immediately started it again. Not just to get the second ending, but because I wanted to. Playing it was such a rich experience. I'm now on my third playthrough and I'm not bored yet.
It's true to say Ryan's death scene is nothing we haven't seen before, but any fiction writer will tell you a cliche is only a cliche if it doesn't work, and it works beautifully here. I must also challenge your claim that there are too many enemies. That's just a silly complaint. And the argument regarding lack of variation leads me to wonder if we're actually talking about the same game.
There are flaws. You're right to say ammo is too freely available. This along with the vita-chambers removes much of the challenge. And the endings are too understated. But this I found easy to forgive, as the beauty of this game is (along with the excellent story) the fun it offers while playing. The fluid gameplay and atmosphere make this a masterpiece of a game.