I like the way the food tastes a little better at Qdoba, but not enough to ignore the efforts that Chipotle is making in its ingredient-sourcing.
If you want Mexican food and you're in the campus area, you could make the slight effort required to head over to South Park Street's Taqueria Guadalajara for a real Mexican taqueria-style repast.
Realistically, though, many will stay on State Street and find themselves choosing between the Mexican-ish chains Chipotle and Qdoba. It's pointless to compare either with a taqueria. Well, maybe that's not quite true. If you're counting calories, have food allergies or other dietary issues, or eat vegetarian or vegan, you're going to find a more welcoming experience at Chipotle and Qdoba. Everything is labeled, every calorie is counted, and you can ascertain that the beans haven't been cooked in lard.
Comparing Qdoba and Chipotle to each other is a popular pastime and a debate I should probably hesitate to enter, but here goes. Both Qdoba and Chipotle feature a cafeteria style line where you can order burritos or tacos with mix-and-match fillings. I say this just in case you've never been to either spot.
The first thing people usually mention about Chipotle is that "it's owned by McDonald's." That's not true anymore; McDonald's unloaded its share in the business back in 2006. Chipotle also differentiates itself with a commitment to using locally grown foods and meats raised naturally without antibiotics. That's true for the chicken and the pork here in Wisconsin, and some locations -- half overall-- also feature naturally-raised beef. 30% of Chipotle's beans are organic, and its sour cream is made from dairy without rGBH. For a national chain to make this kind of commitment to better agricultural practices and to try to buy locally produced vegetables, too, is laudable and probably should be rewarded.
That said, I like the way the food tastes a little better at Qdoba, but not enough to ignore the efforts that Chipotle is making in its ingredient-sourcing. Truthfully, I don't find there is very much difference in the taste of the burritos.
Both chains base the burritos in a cilantro-lime rice that's quite lively. Most of the taste of the burritos comes from the rice and the salsas, so I often choose to go vegetarian. The veggie burrito comes with guacamole and choice of pinto or black beans at both places. Both places have disappointing, sharp-tasting guacamole where the sour cream taste is winning over the avocado. Qdoba has the edge in the salsas, with several more to choose from, including a "fiery habenero" missing at Chipotle.
Qdoba features a couple of special burritos that are worth the effort: a chicken mole burrito and a poblano pesto burrito that get away from the standard red sauce taste and are better than what you get at certain margarita-based Mexican sit-down restaurants in the area. On the other hand, Chipotle's carnitas (stewed pork) filling is the winner as far as either chain's meats are concerned -- tender and rich. Qdoba doesn't feature pork, just chicken and beef.
You can also order anything from the filling bar concocted into a salad or a taco, and at Qdoba, into a quesadilla as well. While the menu prices don't vary much between $5-$7 at either chain, Chipotle's servings are smaller. Usually I'm shocked at the gigantic size of the burritos pretty much everywhere, but the last time I ordered a burrito at Chipotle I was shocked at how small it was. I, who usually take half of a meal home with me, polished off the Chipotle burrito without even leaving a taste for my dog. It was a more realistic meal portion, that's for certain.
Finally, Qdoba has the edge with its nutrition info available online. The calorie, carb, and fat counts for everything on the menu are easily findable, and there's a calculator function so you can dream up your meal your way and see just how much adding the sour cream and subtracting the shredded beef will net you.
Chipotle's nutrition info can't even be found through its website navigation -- I located it after Googling "Chipotle mexican grill nutrition information" and a PDF file came up.