Both Bobrovsky and Theodore are on terrible teams, so no edge either way there.
There are two reasons I go with Bobrovsky, though.
Theodore actually had a decent 2012 season, splitting 60/40 ice time with Clemmenson. It is just he has proven over his career to be very inconsistent. In addition there is still the potential that the Luongo rumors that he might head to Florida, which would put Theodore squarely in the back-up role.
Bobrovsky is much younger and has much more upside. He had a decent campaign in 2011, but really shone in the KHL during the lockout. Easily, he was the best goalie (Arguably alongside Varlamov) in the best professional hockey league outside of north america.