Found plenty of instructions that tell me to do this: Go to Help → Software Updates → Manage Configuration and uninstall it there (they all seem to point to the Mylyn site's instructions). But in Luna the menu has changed. It has "Check for updates" which doesn't have the Manage Configuration option, and "Installation Details." Installation details only allows uninstallation from the Installed Software tab, and Mylyn does not appear there. How does one remove Mylyn from Luna? I would like to avoid uninstalling manually if possible.
I found this blog entry where they want a "lean mean Eclipse machine" without SVN support, Mylyn, and all the other stuff I never use: http://www.martijndashorst.com/blog/2014/07/07/custom-eclipse-luna/ Edit: the above link no longer works.
Unfortunately, in the end they just point you to https://yoxos.eclipsesource.com/, which once was a free, but now is a quite expensive service where you can customize your Eclipse install.