FYI, I posted my problems in another thread, but MY story was a bad O2 sensor.
If you have access to a scanner, check the O2 sensor readings after the system goes to closed loop (engine hot).
The O2 sensor should cross count (readings fluctuate from about .4mv to .8mv rapidly) when you push on the gas peddle.
My bad O2 sensor stayed at about .5mv and hardily moved.
The bad O2 sensor, in my case, caused bad air flow readings to the ECM which in turn screwed with my boost, performance, and gas mileage.
Also worth noting, It took a very long time (couple of months) before it got bad enough to throw a code.
Problems started out small,slight hesitation, stumble here and there, and graduated to a loss of boost and throwing a code,finally.
Not saying this is your problem/solution, but is was mine.

2009 HHR/SS /turbo_upgrade stage 1, 16K miles

 

Yesterday, my SS did this hesitation thing for the first time. I had just rolled into town after a 750 mile trip and was sitting at red light and when I accelerated when it turned green the car bogged and barely moved. After rolling through the intersection and feathering the gas pedal it finally caught. Don't know what happened. The weather was cool as it had just finished raining so heat wasn't a factor. Any thoughts?