A lot of Bioshock 2 kind of went in one ear and out the other, to the point that I don't have any ground-shaking feelings about it one way or the other. Which might be part of the problem. But of what I do remember, here's my thoughts.
First, to concur with what everyone else is saying: yes, a big part of the problem with Bioshock 2 is that it wasn't Bioshock 1. BS1 had a lot of "wow" moments: in graphics, story, and in generating emotion. BS2 basically had the same graphics, and as for the other two, well, more on that in a sec.
There were some things BS2 did pretty well. I said somewhere that I was surprised that BS didn't pull a cue from Clive Barker's Undying and make one hand/button for weapons and the other for spells (or in this case, plasmids.) I don't know if someone heard me, but they did that in BS2, and I think it was an improvement. I'll also agree with whoever said that the "record your enemies on video in action" was a better idea than the original research camera.
But the story... well. In some very real ways, Bioshock was your story; "Jack's" story. You were heading semi-unwittingly into the midst of a war between Atlas and Ryan, but the story was still yours in some real and significant ways, a fact highlighted by your final confrontation with Ryan.
BS2 isn't your story, a point similarly highlighted by the events leading up to the ending. (I don't want to give anything away, but I'll say that there's a certain inevitability to "your" fate combined with a sense of the inconsequence of the physical form that is "you" that puts weight on this view.) One also gets a strong sense that the creators didn't really engage with the philosophy driving Lamb in the way that they did with Ryan. Ryan, in a sense, abided by a kind of objectivism to the point of self-destruction; Lamb, by contrast, seems to drop into a supervillain "ah, screw it, kill 'em all" kind of response that doesn't really reference collectivism at all. There's a fairly obvious irony that no one apparently grasped that Ryan is willing to self-sacrifice for objectivism, and Lamb is unwilling to self-sacrifice for collectivism.
I felt more genuine emotion the first time I saved a Little Sister from her parasite than I did during the entirety of Bioshock 2.
Hopefully, they're on the right track with Infinite.