I have no idea why or how to even begin troubleshooting, but running apt-get update is now taking forever, i.e., about 1/2 hour to list/run. I don't suppose there's a "debug" mode to see what's causing the delay.
I used to have this problem. First of all, disable any PPAs you don't use or need. Second, open the Software and Updates application and pick the "Download from" drop-down menu. Then pick "Other", and "Select best server" option.