Kuki said it very well. The tours offered by the cruise line just waste too much time because they are always crowded.
We were in St. Petersburg, Russia and could have done the usual overcrowded 45 old people on a bus. But we chose to do a brand new Mercedes Benz van with 8 other people - just the 10 of us, so needless to say, we saw a lot more, did a lot more, and went a lot more places. Plus, they were in the museum with one tour guide trying to explain things to 45 people, while our tour guide only had to talk to 10 people. Oh, and I forgot to mention; we paid less!
But as Kuki said, if you plan to see the Vatican, you have to get someone who will pre-book your tickets and help you avoid the very long lines.