You can buy tickets from machines in the courtyard that allow you to simply walk past the long line waiting to get in. We have done this half a dozen times and never had a wait. There was no purse police when we were there, but if your bag is an issue there are free lockers and check room for stuff like that.
I don't think crowds are a problem -- you just push through tour groups that rudely block the way. Some areas are more crowded than others. The very interesting Siberian artifacts, carpets etc on a lower floor were deserted when we were there and there was almost no one in the General Staff Building where the the impressionists are kept. In that huge gallery there were maybe 25 or 30 people in the whole place when we were there.
IMHO the most impressive things in the main building are the Rembrandts -- two of his greatest paintings are in this collection: Sacrifice of Abraham (tell that to Isaac) and Prodigal Son -- just wonderful. The other thing I particularly loved was the gallery of portraits of general in the wars that are featured in the Novel War and Peace -- you felt like you knew these people -- amazing -- maybe a couple of hundred portraits in one gallery with larger paintings of key political figures and generals like the Duke of Wellington and the Tsar.
It is well worth more than a day if you have the time.