Human tides have been flooding into the Vatican every day for several years. It has become impossible to go to the museums on a whim (unless you wait for many hours) For lovers of art history, it is strongly recommended to schedule a visit between January and early March when there are numerous slots available.
But Rome is never as magical as in April or May when Jasmine perfumes the warm air... Alternatives exist. The Eternal City has more than fifty museums and sites, some off the tourist radar.