The first time I was in a place like these was back when I worked at Midway, one opened up in a strip mall near by, ate there enough for overtime dinner back in 01. When I moved I lost that and found qdoba and loved it as much, with the queso even more at times.
When I moved back to CA for 3 years they had Chipotle only down the hill from me so I rediscovered it and was able to get a feel for both. When I moved back here 2 years ago about 6mo later the only Chipotle in town opened up 2mi down the road from my home (luck.)
The point -- I've eaten a lot at both of them. That said, 95% of the time I just want the chicken, not big on beef or pig, but rarely I do get it. On the chicken in both I will get the white rice, black beans mostly (rarely pinto), their hottest salsa, easy sour cream, cheese, lettuce. I don't care much for avacado and I don't get the peppers, if I did I'd go buy a fajita tray.
The base ingredients, the taste (when eating chicken) is the same for all but one thing -- salsa/sauce. That's what will get you in the door. They are both good, don't taste the same, and if you don't mind high fat pigging the queso at Qdoba is damn good but it costs extra.
Here's one kicker if you're into healthy eating -- Chipotle only serves fresh non-frozen ingredients and they're non-processed foods. Qdoba is all frozen and processed foods, so keep that in mind if you are. It's basically a similar taste but one is like eating at a health food joint of sorts, the other is the McDonalds of fast food burritos/tacos.
The price, they're the same. I've eaten both here and they're similarly distant from my place off the same street. The taste until the salsa/sauces is the same too (on the chicken at least.) Serving size, they're the same too, I think it's intentional so they both compete. You will get MORE food if you go with a BOWL over a burrito. Maybe they figure without the tortilla wrap you'll pop for a buck bag of chips to make it up, I don't.
Personally I drive the extra mile for the Chipotle on my street as I prefer the fresh ingredients and I like their hot salsa/sauce a little better than Qdoba, but if I wanted to indulge in the queso I'd go there.
