The GUI for managing plugins in Eclipse got a bit of an overhaul in version 3.4.0. This GUI is accessed via the "Software Updates..." option in the Help menu. This displays the following dialog:
Notice that the option to remove the selected plugin (Mylyn) is greyed out. In fact, this is true of virtually every installed plugin. I know that the Mylyn plugins are optional, so why amn't I provided with an option to remove them?