Well you could complain about it on the MyDefrag forums that the uninstaller leaves too much behind, or start removing stuff with Revo Uninstaller, and at least track the installations.
I seriously don't like it myself when programs install with a version number included in the folder, sort of strange.
I think this is done so if someone installs a new version on top of the old version, custom scripts created by the user won't be lost.
You would think there would be some other way of doing that since you end up with two folders in program files.
Might be nice to have the scripts installed to \program files\MyDefragScripts\Example and \program files\MyDefragScripts\Scripts then the versions in \program files\MyDefrag - now that sure would be helpful. Or at least with each version proved a message saying that these scripts are backword compable with n.n.n version.