Phat Burrito is a home-grown answer to places like Moe's and Chipotle. It's a fun "fast-casual" option in South End with great salads, quesadillas, and burritos. (I haven't tried the tacos yet.)
Their queso is so damn good I'm willing to overlook the chip issue (bagged Tostitos instead of house-made chips).
Go before 10:30am for fantastic breakfast burritos and good coffee.