I wrote a response to this guy's blog. http://www.popmatters.com/post/183201-searching-for-dramatic-stakes-in-the-wolf-among-us/
(SPOILERIFFIC) The relationship between Bigby and Snow is the big thing you're missing here. The choice to burn the tree or kill one of the Tweedle brothers in Ep 3 are important not just because of the Crooked Man, but because of Bigby's relationship with Snow White. Bigby has a strong affection for Snow (I hesitate to call it love). Snow wants him to minimize the mayhem, but burn the tree. Killing the Tweedle brother freaks her out, and refusing to burn the tree damages your relationship with her (I did both, for the record). This plays into Ep 4 as well. Snow wants you to do things her way. She's scrambling around, desperately trying to assert her authority and control in a misogynistic setting that disregards and degrades her. You can side with her or not in regards to both Colin and Toad. Personally, I thought she was asserting her authority in a fucked up manner - we weren't making enough progress on the Crooked Man case, so she took it out on Toad and Colin. I gave Toad some money and tried to stay in the middle on Colin. She didn't like my choices in either situation.
Now granted, this might not be enough for you. I really like romantic subplots in games. But to say that there are no stakes isn't really quite accurate.
Furthermore, there's a strong underlying theme of class. The Crooked Man's empire is vast and resilient because of the massive wealth disparity between folks like Ichabod Crane, Snow, Bigby, Beauty, Beast, and Bluebeard, and folks like Colin, Toad, Holly, Grendel, and the Woodsman. The institutionalized class disparity is exacerbated by Crane's chronic mismanagement. What does it mean for Bigby, who is supposed to enforce this degraded and corrupt system?
The bigger choice is whether or not you are going to enforce order at the emotional and economic cost of innocents (and, as you mentioned, not-so-innocents). As a person who's concerned with these issues in real life, this meant a LOT to me. What does it mean to take down a cartel runner who is committing heinous murders, but fills in the holes in the social safety net for the people you're supposed to be protecting? These are the kinds of questions that the Mexican / US government aren't even considering when they go after organizations like Hamas and the Sinaloa cartel, who do awful things in the name of ideology or business, but aid people who have fallen through the cracks in the system (of the Palestinian and Mexican governments, respectively).
You're missing one of the key elements of the game - that you, as Bigby, may be as culpable in these murders as the Crooked Man, for enforcing a system that creates poverty and renders it cyclical. It's not just a question of catching the bad guy - it's a question of who the bad guy is. We are supposed to ask ourselves if order is a good unto itself, even if order reinforces a corrupt system. It's a question that we, as Americans (I'm assuming you're an American) would do well to ask ourselves.