Of course any choice will have been controversial, but this one focuses on one small aspect of a single conflict that's going on right now. No long term peace, no big views. Chemical weapons? Why this focus? Just so politicians can feel right about having Assad sign the treaty? They can sit back, in the full knowledge they did "something" which has been validated by the Nobel Committee, while the civil war, with all the refugees, killings, injuries and other atrocities continue.
Why not the focus on long term peace? Say what you will about the Rabin-Peres-Arafat prize, but at least they tried to keep a peace process going in a long term conflict and actually improved conditions. (For a while.) And the same holds for the EU, although I have different issues with that one.
(This reminds me: I still haven't updated my CV to include "Winner of the 2012 Nobel Peace Prize". I should do that soon.)
Another thing I'm not happy with: please award it to (a) person(s) next time, who represents a bigger struggle. This is more inspiring to others than choosing an anonymous organization. In this case it's even worse: an anonymous organization most of us have never heard about until the Syrian troubles escalated with a single gas attack. More than the choice of organization, the fact that there is no "real face" we can imagine for the winner hollows out the importance of the prize itself.
Malala would have been perfect in this sense, but I personally would have a different problem with her: it's all too recent. Why not, like with the other Noble prizes, award it years after the fact? See that the effort made sense, improved conditions over the long term. Not "hey, you did something remarkable last year, let's reward it" without seeing the longer term effect. In that sense, seeing the support for Malala and how she continues to inspire people, I would definitely hope for the 2014/2015 Noble peace prize for her.