Currently, if a plugin is selected to be installed (say, plugin A), all of it's recommended plugins (plugins B, C, and D) are treated as required plugins. That is, plugins B, C, and D must also be installed in order to install plugin A, and uninstalling plugin B, C, or D will force plugin A to be uninstalled as well. This is bad because some plugins have many recommended plugins which aren't really useful for the task at hand and just take up memory and clutter the UI. For example, trying to install the "Java Web Applications" plugin forces you to install the entire J2EE stack (because it's recommended) and a lot of other "niche" plugins as well, like "Glassfix 1.x", "IBM Websphere", and "SJAS Identity Management".
To remedy this, how about: (1) altering the plugin install wizard to allow the user to unselect recommended plugins and if possible (2) allowing the user to uninstall recommended plugins later without uninstalling the plugin that recommended it. 2 is not as important so long as the workaround is to uninstall them all and reinstall just the ones you want.