My own Piwik install is practically dusty from disuse (I am tracking 2-3 personal domains that get a few hits a month), but I update Piwik whenever an update pops up. I did the most recent update to v3.0.0, and everything in the update itself went swimmingly (no errors whatsoever). The subsequent DB update itself did not throw any errors, but after it was complete Piwik did throw one warning:
You are not allowed to change the value of the setting “enable_plugin_update_communication” in plugin “CoreUpdater”
I am not sure how this affects my setup, if it is a critical issue or not, nor what kind of a change this was. A basic googling of this warning brought back zero result.
After deleting the folder /plugins on the server and transfering it again, the system is working ok. Before I tried to copy the data over the installation - that failed.