Add span to first level items only

main_menu.php

<?php

function mytheme_preprocess_menu_link__main_menu(&$vars) {
  // first level
  if ($vars['element']['#original_link']['plid'] == 0) {
    $vars['first_level'] = 1;
    if ($vars['element']['#original_link']['in_active_trail']) {
      $vars['active'] = 1;
    }
  }
}

function mytheme_menu_link__main_menu($variables) {
  $element = $variables['element'];
  $sub_menu = '';

  // the $variables['first_level'] will be populated if it is a first level menu!

  if ($element['#below']) {
    $sub_menu = drupal_render($element['#below']);
  }
  $output = l($element['#title'], $element['#href'], $element['#localized_options']);
  return '<li' . drupal_attributes($element['#attributes']) . '>' . $output . $sub_menu . "</li>\n";
}