Control what (super) admins can do. Works with regular and multisite WordPress

not-so-super-admins.php

<?php
/*
Plugin Name: Not So Super Admin
Plugin URI: https://gist.github.com/soderlind/8101b2e45e80b594e9c5
Description: Control what (super) admins can do
Author: Per Soderlind
Author URI: http://soderlind.no
Version: 0.0.6
License: GPL
Tags: multisite, admin

// credit: http://wordpress.stackexchange.com/a/56050/14546
// edit below, save in mu-plugins

*/
add_filter( 'map_meta_cap', 'not_so_super_admins', 10, 4 );
function not_so_super_admins( $caps, $cap, $user_id, $args ) {

	switch ( $user_id ) {
		// Add/remove user id
		case 1:
		case 2:
			// don't remove capabilities for these user ids
			break;
		case 3:
			if ( in_array( $cap, array(
					/* WordPress core */
						'update_core'                // Prevent WordPress core update
					/* Plugins */
						, 'install_plugins'
						// , 'update_plugins'
						// , 'delete_plugins'
						, 'edit_plugins'
						// , 'activate_plugins'
					/* Themes */
						// , 'install_themes'
						// , 'update_themes'
						, 'edit_themes'
						// , 'delete_themes'
					/* Multisite only */
						// , 'manage_network'         // Prevent access to Network Sites menu
						// , 'manage_network_users'   // Prevent access to Network Users menu
						// , 'manage_network_themes'  // Prevent access to Network Themes menu
						// , 'manage_network_options' // Prevent access to Network Options menu
						// , 'manage_network_plugins' // Prevent access to Network Plugins menu
					) ) ) {
				$caps[] = 'do_not_allow';
			}
			break;
		default:
			if ( in_array( $cap, array(
					/* WordPress core */
						'update_core'                // Prevent WordPress core update
					/* Plugins */
						// , 'install_plugins'
						// , 'update_plugins'
						// , 'delete_plugins'
						// , 'edit_plugins'
						// , 'activate_plugins'
					/* Themes */
						// , 'install_themes'
						// , 'update_themes'
						// , 'edit_themes'
						// , 'delete_themes'
					/* Multisite only */
						// , 'manage_network'         // Prevent access to Network Sites menu
						// , 'manage_network_users'   // Prevent access to Network Users menu
						// , 'manage_network_themes'  // Prevent access to Network Themes menu
						// , 'manage_network_options' // Prevent access to Network Options menu
						// , 'manage_network_plugins' // Prevent access to Network Plugins menu
					) ) ) {
				$caps[] = 'do_not_allow';
			}
			break;
	}

	return $caps;
}