Get a copy of Rick Steve's Mediterranean Cruise Ports. It is a great resource if you want to DIY or just to get ideas about what is in the area. Also, check out the Ports of Call board on Cruise Critic for more ideas. Join a roll call over there or search for your cruise on FB.
Here is what my family has done for some of your ports:
Marseille - We took the public bus to the main station, walked to Vieux Port and just spent the day wandering, shopping and eating (we have been to France many times though so did not need to do a big excursion)
Livorno - We docked here instead of La Spezia. We took the cruise line On Your Own excursion. Unfortunately, we were there on Monday when all the museums are closed so we just walked around, checked out the Duomo (super long line so we did not go in), ate lunch and gelato, walked to see the synagogue (which was closed too because it was also a Jewish holiday). We are going on another Med cruise in 2020 and going back to Florence as it is not a Monday and plan to go to the Pitti Palace. Most people want to see David at the Accademia but we are ok not doing this.
Civitavecchia - Take the train into Rome. Purchase a BIRG ticket which also gives you unlimited metro and bus travel in Rome. We spent our day at the Vatican Museums. It is huge and there is so much to see. We were able to do this because we also spent 4 days in Rome post cruise and did not need to run all over the city in one day.
Naples - We took the local bus to Pompei. We did a dIY walking tour using the Rick Steve's book. Spent about 3 hours and then back to Naples for pizza and shopping.
I'm a huge fan of immersing yourself and not trying to do it all. I know a lot of people may never get back to Europe but I think you sell yourself short when you try to cram too much into your day.
