I just ordered a 2013 M3 with the moonroof for two reasons:
1) I live in California and love using my moonroof, night and day.
2) I ordered Laguna Seca Blue which doesn't go well (visually) with CF at all. I would have considered painting the CF roof if the moonroof wasn't available.
I recognize that most people like the CF roof, but I love the moonroof, and am happy it's not an extra cost option like it was on the E46.