Taste: Qdoba has some options that Chipotle doesn't (most importantly, queso), but either way, they're basically the same product. And without the limes at Chipotle and a minor difference in the spiciness of the meats (which goes away once you add salsa), you basically can get a dry mouthful of expensive rice at both locations.
Free Limes: Chipotle has 'em, Qdoba doesn't. This is so important that it gets its own category because it is the difference between that dry mouthful of rice and a zesty, limey mouthful of rice. Take your pick.
Service: Finally, a category to find some concrete separation. While the service at both is basically the same, the workers at Qdoba are a lot more badass. The Chipotle workers smile and talk and are sure to help you when you ask for things. The Qdoba workers might help you if you weren't too scared to ask for anything. That's the type of do-it-yourself service I can admire.
Water (cause if you're spending three extra bucks for soda, you should save the money and go to an authentic Mexican restaurant): Chipotle water comes in a nice big cup, you can put a lime in it and it comes out of the soda dispenser. All standard procedures. Qdoba again proves itself badass, only this time, it's in a bad way. Their water comes in a little plastic glass. You can put water in it, but only if the water spout is feeling kind on that particular day. It comes from a sketchy separate fountain, so you can't sneak lemonade, plus it comes out in such a ferocious torrent it is impossible to fill your cup full, and even harder not to get hit with collateral water damage. It is intimidating, but it's unnecessary thanks to the workers.
Hours: Qdoba is open late at night, Chipotle isn't. This is a big deal and reason enough to make Qdoba your first consideration, because I think we can all agree, having your heart set on one restaurant to fulfill your drunk munchies only to realize it's closed is one of the worst feelings in the world. Ever.
Know of a local food challenge you think Andrew couldn't tackle? Don't want to waste your money on that new place across the walkway from Brats? E-mail Andrew at ajcarpenter@wisc.edu.