Heat issues and whine noise are the big ones. Both can be solved yourself but void your warranty. It is unknown if Apple would fix it for you because they don't seem to want to confirm this problem. Logic would suggest that Apple reads these forums and hear these complaints and will eventually address them before the next revision.
I have both those machines and if it were not for the needed disk space for digital video, I would only have the MBP even with the current problems. My G5 has 8 GBs of memory and a GeForce 6800 GT card. I feel that I have the same power in this laptop minus the memory and hard disk space.