On my second trip to Rome last fall, I had a fellow traveler who was unable to walk long distances so we took the hop on/hop off bus one afternoon. It is true that their routes are limited and most sites are seen from a distance as the buses aren’t allowed into certain areas. It was about $35-40 per ticket which I didn’t feel was worth it given the limited access. If you are mobile, I think your better option is mapping out a walking route from your hotel that gets you to your top sites. Make sure you have a map of some kind that indicates where the city’s taxi stands are located in case you want a ride back to your hotel.