Just thought I'd share a few ideas I had for UI improvement and one new feature.
Making it sort sites alphabetically (currently in order added) would make it easier to find and add a site among many others.
Hide Stat Url:
This would be a new feature that made use of the ability to hide piwik server url via this script: http://piwik.org/faq/how-to/#faq_132. It could be radio no/yes button that when clicked yes, would display a sentence or two of instructions below on how to install and it would also change the code displayed in tracking settings below to reflect changes (all piwik 3 url references replaced with site url).
The option descriptions are not lined up correctly, so it's confusing which checkbox is for which option.
Statistics View Settings
It's not clear from the descriptions the difference between dashboard data and board chart.