The Pope called 2000 A.D. a Jubilee Year and many improvements were made to ensure that the thousands of pilgrims would be taken care of. Hundreds of volunteers in blue vests are willing to point you anywhere. Not all speak English so be prepared to be tossed between a few before you get your question answered.
The Jubilee door on San Pietro is open and you can walk through it. It will be closed at the end of the year and will stay that way for another 25 years.
Even with all the pilgrims trying to see the Pope, who shortened his traditional summer-long vacation to give mass and entertain pilgrims, Vatican City has done a marvelous job moving people around. It will be crowded, but not overly crowded, and nothing unusual compared to some of the other sights in Rome.
If you aren't interested in seeing the Pope, ask at any of the TIs for information on when he will be appearing and plan around his appearances. If you have a chance, go to Vatican City in 2000 before the volunteers go home and the fabulous art is hidden by scaffolding.