The pavilion is the most important part of a faceted stone to get right. If the angles aren't right, the stone will look lifeless, with no fire or sparkle. The crown is a little more "forgiving" in its angles. With all that said, the pavilion is typically cut first for this reason...
Personally I've cut stones both crown and pavilion first, and though i have no problems with either way, i prefer to cut crown first...i find it just a smidge easier in the transfer of the dops. I think the main factor to consider is (does one have enough height to the stone to begin with prior to cutting.)
My only other advise is try cutting both ways and see first hand what works best for you... Enjoy!