Hope this helps others in their trip planning. Just came back from our June sailing. It was a great cruise, we (family of four) did not want it to end, it was our first time in Europe.
Arrived in Rome (FCO) at noon on Friday, and took the pre-arranged shuttle from the B&B (1 km north of the Vatican) we were staying at for 37 euros.
On the Friday afternoon, walked to the Vatican (had pre-purchased Vatican Museums tickets online from the Vatican website before leaving).
Visited the Vatican museums, very nice 2-hour tour, the guide spoke English but with a strong accent.
Exited the Sistine Chapel using the right doors at the back for the shortcut to St.Peters Basilica.
Then purchased the 5 euro tickets to climb up the 550 stairs of the St.Peters Basilica, to the top of the dome, great views on the city from there. Then walked back down to visit the Basilica.
On the Saturday, took the Hop-on Hop-off bus to the Colosseum. We had pre-purchased the hop-on hop-off bus tickets for Rome and Messina.
In hindsight, I would have taken the subway/metro or just taken a taxi and have them stop a few minutes at key spots (eg. Trevi fountain, etc) on the way to the Colosseum.
Purchased the ticket for a group tour (25 euro pp) from a salesman in front of the Colosseum, it also included a guided tour of the Forum.
The Colosseum guide again spoke English with a strong accent, she had a bit of trouble finding the right English words/phrases.
The guide for the Forum was great, his name was James (from England I believe, and his accent was not a problem, he was doing this for free as advertising for his new business offering Vatican tours).
Took a taxi on the Sunday to the Termini station, and then a train to the port of Civitavecchia at 9 euro, and then walked to the port (note there are stairs at the Civit. train station)
A good website for newbies to Rome is www.roninrome.com, includes lots of info on getting around and using trains, etc.
On the Monday, we took the hop-on hop-off bus tour of Messina (CitySightseeing, pre-purchased with a 25% voucher/discount coupon from moneysupermarket.com)
We felt that we needed an down day after visiting Rome, and did not bother to book a more pricey excursion.
Visited the 2 churches near the port (Cathedral of Messina (Duomo), and Annunziata dei Catalani Church), both churches are 2 meters below street level since they survived the devastating earthquakes, which levelled nearby buildings and were rebuilt on top of the rubble.
We could have taken a taxi for much cheaper to visit the Tempio Votivo di Cristo Re.
For the Tuesday (day at sea), make sure to grab a patio chair after breakfast, otherwise you'll be out of luck.
For the Wednesday, we had reserved a tour with ephesusshuttle.com ($76pp for 4 persons, tour 4 including the terrace house), you only have to pay after the tour is done, the shopping at Ephesus is not the best.
For those who want to buy souvenirs or do some shopping, the best prices can be found near the port of Kusadasi, if you cross the street there are lots of shops crammed together on the street incline.
For the Thursday I visited Athens on my own, my wife and teens took the cruise ship excursion, since they were concerned it would be too hot.
(they took the Bus tour of Athens + Plaka shopping at $59pp, the cheaper $39pp Bus tour of Athens was sold out), the cruise ship docked at terminal B (south east part of the port, and the furthest from the metro station)
Before doing Athens on my own, I had downloaded the free MP3 audio tours from Rick Steves (http://www.ricksteves.com/news/audio-tours.htm) and saved them on my smart phone.
I took the free shuttle to cruise terminal A, then walked down (you can also take the 843 or 859 bus, since it is a good mile) to the Piraeus metro station, and took the metro to the Thissio station
(if you take the bus/metro (combined ticket is 1.40 euros, good for 90 minutes), don't forget to validate your ticket)
From the Thissio station, walked to the Ancient Agora and purchased a 12 euro ticket (which also includes access to the Acropolis, Dionysus Theatre, Acropolis museum, etc),
After the Agora, I made my way to the Aeropagus (Mars hill) where the Apostle Paul preached, and then on to the Acropolis, the Dionysus Theatre, Hadrian's Arch, the Temple of Zeus,
and then walked to the Olympic stadium, and then back through the park to the Syntagma metro station, and back to the cruise port via the blue line metro to Monastiraki and the green line to Piraeus,
and then took the 843 or 859 bus to the cruise terminal A, and the free shuttle to the cruise ship (at cruise terminal B).
For those who want to shop, the Plaka is located between the Acropolis and the Monastiraki station.
On the Friday, the ship docks at Souda (there is nothing to do or see there), we took the 3 euro return bus trip to Chania, and then walked to the water front, (some other cruisers we met were going to take a taxi to the Chrisi Akti beach which is apparently nice) we visited the Maritime museum (3 euro pp) but was disapointed that there was no english explanations or signs, after some shopping, we took the glass bottom boat tour with some snorkeling (25 euro for 3 persons) with http://www.captainnickchania.com/, there was nothing spectacular with the fish you see, but it was nice to refresh in the Mediterranean sea, and still well worth the price. There was one shop that was selling nice baseball style caps for 6 euros near Captain Nick's boat.
On the Saturday, another day at sea, make sure you get a chair after breaky. Registered for the adult soccer tournament, but they only had 2 balls left, and they soon went over the side of the ship, so did not get to play.
After deboarding the ship, we took the reserved shuttle (www.romashuttle.com) back to FCO airport (we had found another family of 4 on this board to share the shuttle with before the cruise).
Btw, tried to get some euros from the ATM on the ship, that machine hardly ever works, it worked once out of about 10 attempts to withdraw (2 cruises now with RCCL that the ATM is almost useless), your best bet is probably an ATM on shore.