Chipotle is better by a landslide, that's not saying Qdoba is bad, it's just that their tortillas are really gummy and sticky, the food is cooked well, and they have queso, but Chipotle is the whole package.
Having lived a year in my dorm right beside a Chipotle and across the street from Qdoba, I must say that Chipotle ain't ship when compared to the lovely Qdobes and their queso.