Well, if you look at early BSI footage and how the game ended up it's obvious that their initial vision was taking too long and they were "encouraged" to move the game along for release. This could very well have to do with this decision.
If you watched early footage and interviews about BSI then you remember that Elizabeth was supposed to be this super important character that would help you in numerous ways. In the old footage we saw this in the form of her augmenting your vigors. In one scene Booker is fighting one of the Big Daddies (I forgot what they were called in BSI) and he TK's a bunch of items, she then heats them up and turns them into a huge ball of molten metal that Booker tosses at the BD. In another scene we see her open a rain cloud and soak about 20 enemies which Booker then electrocutes.
None of this was in the final game, neither were a bunch of other scenes (although these could have just been "concept" scene to keep us guessing about the story, but I doubt it) enemies and encounters. In the end Liz just ends up being a minor criminal (lock picking) and scavenger (health/eve/ammo/money).
So it would not surprise me to find out that 2K pushed them to make a finished product and all the really great ideas had to be scrapped. This would also fall in line with the slow release of DLC as Ken and Co. probably weren't to eager to put more work into a game they didn't feel was theirs to begin with.
In the end tho this is a great move for US, because if Levine can get into a position where he's delivering smaller, more focused games directly to us, with our input then we're sure to see some of the best gaming entertainment in the history of the hobby.
P.S. Bioshock 1 (Story/Characters) > Bioshock 2 (combat/endings) = BSI (combat/characters)
That's my ranking including the best parts of each, IMO of course.