I have one shop that is at the limit for number of unique items - 2500. When I try to autoprice, it takes so long! Each step of the autopricer takes a good 2 or 3 minutes. I expect it to take longer given the number of items that it has to go through, but not a solid 10 minutes of my day.
I've also noticed that if you get a sidebar alert during the final stage of autopricing, the autopricer will stall out.