When we started doing agile (and then "Agile" ... ugh) development the entire process broke down. There were no (good) plugins that could do kanban and moving features from state to state to state dramatically increased the size of an items log. That, along with the friendly, and then suddenly not so friendly filtering lead to our team dropping the product and moving to Jira.
While Fogcreek's "Fastbugz" was a gallant effort in modernizing the application stack and speeding up page loading time, it fell short as it didn't functionality support feature _and_ bug management.
I should note, we had reached out to Fogcreek with all of our requests and critiques but they weren't interested in hearing us out passed the usual account or customer service manager.