There's two ways to look at the Bioshock 2 story. One is that it's a lazy piece of trash ripoff of the first game and blah blah. I'm not sure where this comes from, but a lot of the common internet opinions completely baffle me as well, so I gave up trying to figure it out.
The other way is that it's portraying the exact opposite end of the extremist scale from Bioshock 1. Jack basically had no agency in a group of people who had plenty. Delta has tons of free will among others like him who have none. Andrew Ryan was the absurd pinnacle of objectivism deconstructed, while Sophia Lamb was just as nuts on the collectivist end of the scale. The end result for each was the same, but the illustration of both plots was how they got there through different means. I saw Bioshock 1 and 2 as bookends, though 2 was already at a disadvantage simply because people had seen Rapture before, so now it all "felt old and boring" I guess.
I also wasn't a big fan of how 2's moral choices were dictated to me, but that leads into the morality systems debate, so I want to shill for another game that did morality right:
Alpha Protocol.
There are choices, and they involve levels of morality, but the game never gives you "goody two shoes" or "Snidely Whiplash" points. You can do horrible things without repercussion, or choose to atone for them, or try to be a good guy, but at the end of the game it all plays out as a story. Not about heroes or villain protagonists, but as a guy in a very morally gray world who probably made some very ambiguous decisions but managed to come out on top. There's only one character who usually comes off as EVIL but you can actually beat him at his own game, potentially making your character just as "evil" but not once does it involve kicking a puppy.
Anyway, I recommend it. One of the best-written and least preachy games I've played.