I had this plugin installed on an old blog and recently updated both WordPress and the plugin.
After that the admin page under Pages disappeared. I looked into the code and here is what you have to change in order to make it work again:
On line 108 from wppagetree.php replace
add_submenu_page('edit-pages.php', __("WordPress Page Tree", "page-tree"), __("Page tree", "page-tree"), 7, __FILE__, 'pagetree_options');
add_submenu_page('edit.php?post_type=page', __("WordPress Page Tree", "page-tree"), __("Page tree", "page-tree"), 'edit_others_posts', __FILE__, 'pagetree_options');
First is the "edit-pages.php" - now it is "edit.php?post_type=page". Then the plugin is using user_level when these have been deprecated a LONG time ago... - substitute with "edit_others_posts" capability which corresponds to the "Editor" role and higher.
Additionally you can comment/remove line 47:
wp_enqueue_style( 'page-tree-css', plugins_url('page-tree.css', __FILE__), false, false, 'all' );
Since this file actually doesn't exists(not sure if the dev missed it or it's supposed to be like that) - you'll save yourself a 404 error from the admin section :)