I really don't understand all the guilt in liking Chipotle! If you like it, you like it. Frankly I'd take a tasty inauthentic chain restaurant burrito over some of the local flavorless grease bombs any day. I think the success of Chipotle is down to their very focused menu. They only serve burritos, salads and chips. They have chosen a narrow scope and do it well.
Like most chain restaurants, it usually tastes better the when they are busier. I have gone at off-times and had less-than fresh ingredients served to me. Frankly though if they start scraping the bottom of the container of meat I imagine you could politely ask to wait for a fresh batch.
I'm not a fan of grease and I enjoy the fact that the meat seems lean but juicy. That way grease isn't squirting all over your plate as you attempt to eat the burrito. Their chips are generally very fresh tasting and warm. They have just the right amount of salt. I'd recommend the guacamole as it's certainly better than I ever imagined it could be.
There are better sit-down restaurants to eat Mexican in town. But if you need something quick to eat and are near campus this is a great choice over somewhere like Taco Bell.