I have a 2006 X3 with the moon roof, and I love it. There was no penalty regarding headroom (I'm 6'7").
I hope to never own a car without a moonroof ever again.
besides: on the rare days that I ever use the air conditioner, opening the roof to get the hot air out of the car for the first mile driven is a bonus.
Center of gravity? Give me a break ... unless you race, this isn't an issue.