I came to this forum for advice and thought I would follow up with what actually worked for us.
We were in port on Sat June, 8. Our in port time was listed as 7am -10pm. We walked off the boat right at 7am. Took free shuttle. Port Mobility doesn't start until 8am. Walked 1 mile to train station following crowd and signs. It seemed like more than a mile. Arrived 7:40. Bought 5 zone birg for 12.00. Took 8:01 regionale. Arrived 9ish depending on where you get off. We were going to the Colosseum first. We bought our tickets on the official website exactly 30 days in advance and had to get up at 2 am to get in the queue to get them. We were able to snap 10:30, but 10 would have been ideal. Anyway when we got off the Regionale we road the underground B -2 stops. Download rick steves tour if you don't get the audio in your package. It was excellent. Entry was fast with the tickets bought ahead of time. Make sure you have your passport. Side note if your ticket is 11 is for Colosseum, get off at Circus Maximus and walk by it and in the Roman Forum before the Colosseum. It gets crowded later. The line to get into it after the colosseum was VERY VERY long.
If you don't do the official tickets several people on our train in had a city pass. No idea if it is better or not it just seemed to be popular with those touring on their own. It included a HOHO.
We had a 3:30 tour time for the Vatican Museums. We reserved those 60 days in advance. In between the Colosseum and the Vatican we were able to see the Trevi fountain, Spanish Steps, Pantheon. After the Vatican. We went to the Sistine Chapel and St. Peter's pretty much moving with the crowd. It was crowded.
All in all we walked 13ish miles and listened to 4 Rick Steves guides.
Took regional 6:32 from S Pietro to Civitavecchia.
We planned to take the Port mobility, but a taxi van was at the station and it was offering the same price. We rode with a few others. It was fast and easy.
