I'm not enough of an expert to provide an exact diagnosis and solution. however, I can provide some ideas to look into if no one else comes up with something better later.
if it runs than it is getting air, fuel, and spark. if it is running rough that it might not be getting one of those things properly. you have new spark plugs and air filter. it might be worth running a bunch of fuel cleaner through your fuel system to clear up any carbon deposits that might be in your fuel injectors.
the symptoms you're talking about can also be caused when the piston is having a hard time pushing air out of the cylinder on the exhaust stroke. the most common cause of resistance like this is the catalytic converter. even before the material inside is all used up, the cat can get clogged and begin to obstruct air flow. Even without a cat these modern vehicles produce better emissions than vehicles did when emission regulations where first put in place. you can drill out the material in the cat and use an adapter to shield the down stream CO2 sensor.
unfortunately, the turbo could also be an issue. this is something that is difficult to verify without spending a couple hours taking the turbo off of the car and visually verifying the inside of the exhaust side of the turbo. shops won't do this unless they have ample reason to expect that the turbo is bad. they won't do it because they will charge you for that time and they likely have nothing to show for it. your symptoms could be cause by the turbo blade spinning off access. no real problem is going to be visible until the turbo blade wobbles so much that it contacts the inside wall of the turbo housing, or until the turbo starts leaking oil or coolant.
any time you do go into the shop, ask about the PCV system. the multiple valves in this system are very common failure points in the 1.4L ecotec power train. any failure will not stop the car from running; but can cause symptoms like rough idle, lower power, and burning oil.
hope this helps!