Making menu wrapped in nav tag
Did you read this and this posts? I thinks it's not so difficult to achieve this:

function MYTHEME_links__system_main_menu($variables) {
  $html = "&lt;div&gt;\n";
  $html .= "  &lt;nav&gt;\n";
  foreach ($variables['links'] as $link) {
    $html .= "&lt;li&gt;".l($link['title'], $link['path'], $link)."&lt;/li&gt;";
  }
  $html .= "  &lt;/nav&gt;\n";
  $html .= "&lt;/div&gt;\n";
  return $html;
}