There is a website www.roninrome.com that I found very helpful for advice on visiting the Vatican museum, I advise you to take a look for some hints on visiting the Vatican. We followed those ideas and we had no difficulty getting into the museum. Do look at that website and that should help you.As I remember it we reserved tickets online and walked up to the inside ticket booth with no problem.
That being said, inside the museum was, literally, wall to wall people, somewhat similar to walking on any New York City sidewalk during rush hour. The long corridors displaying tapestry and the one displaying world maps were particularly bad. We zig zagged around people without being rude, but with intent and moved on out of those areas as quickly as we could come, barely looking at the walls, unfortunately, but under the conditions that's what we chose to do. We were there in April, I believe on a thursday, arriving at about 130 in the afternoon.
I also wanted to mention that prior to our trip we downloaded the Rick S Steves' audioguide for saint peter's basilica and found it very worthwhile.
In any situation, expectations can be everything, so if you prepare your psyche for crowds, you will still be able to enjoy yourself at the Vatican. You might want to do a little research, identify 5 or 6 pieces that you would really like to see and then when you arrive go directly there finishing up with the sistine chapel. Enjoy!