I'm currently using CO2 since my old pump wouldn't mount cleanly on the new bike...didn't want to risk scratching the carbon....but I feel a little at risk. I carry two cartridges and tubes, and have the same in my wife's bag, but twice in the last four years, I've had situations where either my wife or I had two flats on the same ride. It already seems like we're carrying a bunch of spares, but don't feel comfortable with less.
Bottom line...CO2 is quick and easy, pump is reliable can't be emptied. I agree with the other posts that the combo pumps are probably the best of both worlds, even with the limitations that the pumps have.