I've debated this topic with MANY a person. I'm not exaggerating, this is a legitimate source of conflict between people here.
As to which is better, I've eaten at both hundreds of times and I can definitively say that Chipotle is the superior option. Chipotle is much better about seasoning their meats, their salsas, and their food in general. Additionally, the tortillas are handled differently resulting in a more robust wrap for the good stuff while Qdoba's have a tendency to be overly soft, bland, and fall apart. The only thing Qdoba has over Chipotle is the addition of the queso sauce, which adds an interesting element, but they're inferior in every other area. That extra bit of cheesy spiciness doesn't make enough of a difference to secure the victory.