Open up the install.php script and locate the following piece of code:

    // array with names of plugins to install. Plugin files must be present in the 
    // nucleus/plugin/ directory.
    //
    // example:
    //     array('NP_TrackBack', 'NP_MemberGoodies')
    $aConfPlugsToInstall = array();


    // array with skins to install. skins must be present under the skins/ directory with
    // a subdirectory having the same name that contains a skinbackup.xml file
    //
    // example:
    //     array('base','rsd')
    $aConfSkinsToImport = array();

This code is all you need to change: list the names of the plugins and skins you want to auto-install in the arrays.