I'll be the one to disagree about using ship's excursions.
I've done it both ways, and find much time is wasted on ship's excursions. Take a tour with lunch and it takes an hour to an hour and a half out of your very short time in port.
The tours through many important sites move only as fast as the slowest person in the group.
For most major sites it's not difficult to book a particular time for a private tour, to bypass the lines. Often we've gone to visit such sites, and pass the cruise line tours lined up waiting to get in.