i agree with you that the whole SAVE..OR KILL??? little sisters thing was fundamentally meaningless and the ending of the game was probably the worst about it because the only difference between A and B was your choice of terrible end cutscene which had absolutely none of the thematic depth of the rest of the game. the only reason little sisters choice could have worked better is if it had some fundamental impact on the narrative of the game which would essentially require them to make two scripts and alter level and design choices on a very basic level for each way the game developed, and would be very hard to write effectively. GTA IV
tries to do this but fails spectacularly IMO because it doesn't actually affect anything but, once again, the shitty ending since it narrows it down to just a series of A... OR B choices which start and end at the same points. if the GTAIV team, probably the absolute best game design team ever assembled in the world except for maybe the guys at Valve, can't do free choice right, then there's an argument there that it's something which isn't even close to being done exceptionally well in the current generation of games.
however i wasn't even thinking so much in terms of PLOT FREE CHOICE but yeah, walking around rapture. why does it matter whether the actual level design is linear or freeroam as long as each section begins at point a and ends at point b? i'd argue that freeroam is almost invariably better, because it gives more of a sense of scale and more options for the gameplay than linearity. plot linearity can be used very well - but my difference of opinion here isn't that it should be GRAPES OF WRATH CHOOSE YOUR OWN ADVENTURE EDITION (good idea ..lemme call my publisher) because games and lit are fundamentally different mediums.
it's a gameplay, not a narrative, choice. you can still have focused objectives, great setpieces, characters, etc. in a game where you're able to wander rapture. i'm not talking GTA IV
lets just wander rapture killin cops fuckin around smokin weed type free-roam. i'm saying that if you have to start from the bubble craft at dock a, and go to exit at point b, and the designers have decided you must 1) have a conversation with NPC at point C, 2) restart the power for a door at point D, 3) defeat a boss, there's no reason why the sequence of events has to be A-1-2-3-B, and not A-1-2-3-B, or even 2-A-1-3-B or whatever, and there's absolutely no reason why it should be a straight line from A to 1 to 2 to 3 to B. because it's far more interesting if you're thrown into, i don't know, RAPTURE SHOPPING DISTRICT, and you have 4 or 5 choices to progress through the level and multiple areas you can explore (some of which may even be mutually exclusive). this is the difference here, because i believe that you can accomplish this and still have the same intact narrative the whole way through without it necessarily being jarring as long as you don't slip into the 'this is the exact pattern of how every level will progress' formula. dead space did that with the 'you have two objectives on this level of the ship, so complete one, backtrack, complete the other, backtrack, board a train' thing, and far cry 2 for all of its claims of being entirely open ended had a level design structure that may as well have been Doom for how amazingly repetitive and linear it was (meet your buddy, who has the same dialogue as every other buddy; accomplish the mission; save your buddy from evil africans, end of mission, repeat).
avoiding gameplay linearity isn't something which is beyond any kind of technical limitation and has been done by lots of games at this point better than how bioshock did it; and certainly which splicers you kill in which order or which room you explore when has little effect on the narrative unless it's a plot event, in which case it should forcing you into a bottleneck to see that event anyhow.
i'm not advocating some type of fanciful DO..DO WHATEVER system; i'm just saying that a game with bioshock's level of effort into production design, etc. has no real excuse to be so linear from just a gameplay standpoint other than if they couldn't find the time to do it (which they probably could have if it was a priority from the start), but even so, i'm not DISSATISFIED with that aspect of the game if it means that it didn't try and fail horribly at it and in doing so destroy the game. my real objections are similar to yours on the illusion of moral choice thing.
there was a fascinating blog post i read that had a really interesting idea for what should have been the end of bioshock which really made me think a lot though about the whole horrible ending and CHOOSIN WHETHER TO KILL BABIES how it really failed on a fundamental level within the game. i'll just quote the part which i found really cool:
Bioshock does a superb job of putting us in that very position of pseudo-choice. We act on what we know, but what we know is fed to us by those with agendas. So we think we act freely. But how can we Randians act on what they call "rational egoism" when all knowledge is only true or false relative to a subjective being, either ourselves or others? How can rational egoists say that pursuing happiness you don't deserve is irrational when we rationalize what we deserve? Or in the case of some characters, it's rationalized for us.
The beautiful irony presented in this game is that the game itself is an objectivist work of art. Objectivists believe art is one’s perception of reality made into something real and physical so that everyone can see and participate in your conscious mind. Bioshock does just that. Ken Levine and his team have made what is their "perception" of what a place like Rapture would be like in reality, based on our own reality. Rapture, in a world with the values and people we know, ends up the way we expect. In other words, the creators of this game has made an objectivist work of art pointing out the reality that objectivism is not realistic.
The game for me was absolutely wonderful, but its ending was disappointing in how little it left to ambiguity. It departed from its discussion of the complex self-destructiveness of freedom. I would say it cheesed out, especially leaving the fate of Tenenbaum mostly unresolved. I propose a better ending.
As Atlas lies defeated before Jack, you are given a minute to choose to kill him or save him while he utters the last words "Would you kindly save me?" Failing to choose and he dies. Choosing to let him to die carries out revenge fantasies for "the good guys." Choosing to save him means doing his bidding. Which choice you consider to be truly free will always be subjective. Here, I would turn off the game, and start playing this wonderful tale all over again.