All of this is just window-dressing for the story of Booker and Elizabeth. It's not supposed to be about the city, or the political themes, it's about a man and his daughter. These things are all underdeveloped because they're not the point.
But by the time the nature of the reveal rolls around, it's too late for Booker and Liz to re-establish their bond as father and daughter before the whirlwind of the ending kicks in.
There's no little moment of downtime such as the ones that occur while going through the Hall of Heroes, Fink's elevators, or what have you for Liz to express her thoughts. She obviously realizes that something is up, or that some old memory she has along with Comstock's ravings has triggered something in her (and this is before the siphon is destroyed), but we as Booker aren't ever allowed to experience it with her.
Instead, we're slogging through the final airship battle.
I understand Ken's moving the Twist to the end, since it's extremely central to the narrative, and (officially, narrative-wise) revealing the father/daughter angle too far before the timeline information comes into full effect would make it harder for us to see Liz doing what she does. Still doesn't make their newly found out father/daughter relationship particularly compelling at the end. The hints are there, but nothing comes of it due to timing issues.
Getting back to Liz, her main 'arc' mainly consists of viewing the growing insanity of Columbia and how it changes her as a person (in addition to the whole "who are my parents and how does that affect me" discussion). But this ties back into the whole 'exploring too many themes' argument, as we're constantly bombarded by different images/messages of differing experiences, and since we as Booker may not be looking in the right section, or focusing on the impending gunfight, Liz is forced to react to each and every one of them to make sure we catch them, which at times is completely missable.
The player is the one who assigns the weight to things like the Guitar scene and Liz's development. And while I did enjoy Liz coming to terms with the crazy situation she'd been raised in and how that continued throughout her life (which was what I presume was supposed to happen, as to better allow the player to not 'fight' Booker's decision to let Liz kill him) personally, the guitar scene and a few other 'connection scenes' didn't really mesh with me, because instead of being naturally occurring, they felt 'forced' in a way.
edit: I'm not saying that Liz and Booker don't bond as two people, a grizzled wordly resecuer with the knowledgeable, non-helpless rescuee, but to me, at least, that's so much less interesting once you know of their real connection to each other.