Send email with html template programmatically
In the mimemail-message.tpl.php info you can read


  Copy this file in your default theme folder to create a custom themed
  mail.
      Rename it to mimemail-message--[module]--[key].tpl.php to override it for a
      specific mail.


Try to change your tpl name from 
mimemail-message.tpl.php to mimemail-message--system.tpl.php