After a string of negative experiences we have taken the Vatican Museums and the attached Sistine Chapel (you cannot visit the Sistine without going through the maze of the museum) permanently off our list of things to see and do in Rome, until they either change things in a major way at the Vatican or they restrict the number of tourists allowed in at any given time.
For more information, visit Trip Advisor, key in Vatican Museum, and look at the bottom three levels of commentary.
We do our best to help our guests avoid tourist traps and negative experiences. There are dozens of churches and smaller museums in Rome where one can enjoy classic art without feeling like a sardine. We will be happy to take our guests to these places so that all may have a more enjoyable experience. Entry to the Cathedral of St. Peter does not require passage through the Vatican Museum, and so, we are happy to take our guests to this place.