As for the location of the hotels/apartments in Rome, my experience is it should be somewhere around the Vatican City. Rome is different from Istanbul, Turkey, in many ways. One of them is that there are different types of the towns in Istanbul:  old town, where the historical sites are, and new town, the modern city. Hanging out in the old town, I could get to the sites easily without bothering the public transportation. Rome, on the other hand, is not like Istanbul, all the historical sites there are scattered in different regions. I had to decide which region would be the major one to stroll around.  After the researches, I thought I should, for its rich and vast collections, spend more time in Vatican City, which left me no other option. I had to find an apart. near the San Pietro train station after my disembarking from the cruise ship at Civitavecchia.

Of course, it could be either viewed as being good or not so good, It depended upon the way you looked at it. My point was that staying in around this area offered my wife and I a great convenience to roam over the Vatican City area again and again. With its location nearby, the whole Vatican City and the Castel Sant' Angelo would be all in the walking distance, 10-15 minutes at the most.

Rick Steve, the author of Mediterranean Cruise Ports, is right that there are always so many people waiting to get into the basilica in the daytime. The best hours to visit the basilica, therefore, would be late in the afternoon, 3.30-6.30 pm. (The basilica closes at 6.30 pm.) Taking his advice; we stepped into the St. Peter's Basilica in the late afternoon without any hassle.

We had visited the basilica for 3 times during our 7-day-staying in Rome totally. 2 times were all in the late afternoons so we didn't wait long to get into the church. (And there were not many people inside either, which meant taking pictures was pretty easy, too.)

Next day, we went to the Dome and spent whole morning there. It was my first time to see the Saint Peter Square from the dome. It's so amazing and breathtaking. After that, the elevator took us down directly into the basilica from the Dome. That was our 3rd time to pay a visit to the church. We then used the rest of the day wandering about in the Vatican Museum and its garden. The museum was definitely a must-see. You will need plenty of time to get a full view there, at least 4 hours.  

On the other hand, it would be a bit too far to go to the other historical sites from this area. We took, however, buses, #31 or #32, from where we stayed to get to the subway station, Ottaviano, and it then took us to Termini Station or anywhere we liked to go. (Or you could get on hop-on-off bus near the basilica as an another option to travel around in this great city. The best sightseeing bus would be 110, by the way.) This is what I meant that this location could be viewed as being either good or not so good.

In short, I think it is a smart and right choice to stay in this area, especially if you have many days in Rome.