Bye, bye region.tpl.php and block--system--main.tpl.php

template.php

<?php

/**
 * Implements hook_page_alter().
 */
function mytheme_page_alter(&$page) {
  // Remove all the region wrappers.
  foreach (element_children($page) as $key => $region) {
    if (!empty($page[$region]['#theme_wrappers'])) {
      $page[$region]['#theme_wrappers'] = array_diff($page[$region]['#theme_wrappers'], array('region'));
    }
  }
  // Remove the wrapper from the main content block.
  if (!empty($page['content']['system_main'])) {
    $page['content']['system_main']['#theme_wrappers'] = array_diff($page['content']['system_main']['#theme_wrappers'], array('block'));
  }
}