I think the stock brakes are pretty outstanding, for the most part.
Unless you are tracking the car, like djnelsen said, stock brakes are more than sufficient for at least up to Stage II, IMHO. Hell, I've put 10+ track days on my stock brakes, and aside from the multiple sets of rotors/pads (thanks, warranty!) and the end of the day fade that I had, they were allstars out there.
Having said that, my next mod will quite possibly be a front/rear Alcon upgrade, but that's only if I keep the car.
My personal order was: chip, suspension, wheels/tires, exhaust. And probably brakes next.