I think it would be a good idea to let the users choose where they want their trackers files to be located.
For instance, Piwik admin could be installed in /administration/piwik
and the trackers in /
Why I want to be able to move the trackers is very simple : improve security. I’m sure the Piwik team is doing their best but anyway, I want to put the trackers in a public place, and have ALL THE OTHER FILES in an Apache protected folder (by password, IP restriction or whatever).
Also, it would be good to be able to change the trackers file names to circumvent blockers. This might be an option offered only if statistics are anonymized if it hurts you ethics. As a webmaster I want accurate statistics but I have no interest in tracking users as individuals, so… dodging blockers in trade of partial IP would be fine for me.