Advice on plugin structure

You should limit your helper functions. In a rather big plugin I am writing currently (~50 classes) I have just three helper functions, placed in the plugin main file:

/**
 * Delete plugin option on deactivation.
 *
 * @return boolean
 */
function t5_delete_option() {
    return delete_site_option( 'plugin_t5' );
}


/**
 * Load a class from /inc/ directory.
 *
 * @since  2012.10.26
 * @param  string  $class         Class name
 * @param  boolean $create_object Return an object or nothing
 * @return bool|$class
 */
function t5_load_class( $class, $create_object = FALSE ) {

    $path = plugin_dir_path( __FILE__ ) . "inc/class-$class.php";

    if ( ! file_exists( $path ) )
        return FALSE;

    class_exists( $class ) || require_once $path;

    if ( $create_object )
        return new $class;

    return TRUE;
}

if ( ! function_exists( 'pre_print' ) ) {

    /**
     * Print debug output
     *
     * @since  2012.11.03
     * @param  mixed
     * @return void
     */
    function pre_print( $var, $before="" ) {

        $export = var_export( $var, TRUE );
        $escape = htmlspecialchars( $export, ENT_QUOTES, 'utf-8', FALSE );
        print "$before<pre>$escape</pre>";
    }
}

All other classes are placed in a directory /inc/ (not my choice, I have to work within existing rules for that).

The file structure should reflect what the files are for, not where they are used, because that can change any time.

Implement a main controller class that loads the files you need in your current situation. So have to look at one place only to see what is going on.

The main controller collect some data (plugin URL, current user’s IP address, an instance of the custom database class …) and passes these data as a property list object to the called classes. So there is never a need for global access to anything besides the class loader (I don’t use an autoloader) and the tiny debug function.