It was slow, full text searching didn't work (literally), when using their API to delete repos and recreate them there would be race conditions that would leave us in a state where their support would have to go data spelunking on their end to correct them.
I could nitpick the GUI and such but the real issues were these fundamental problems. I was shocked. This happened for years.
http://www.joelonsoftware.com/articles/fog0000000024.html