Joomla registration emails need some decorating,
How do I edit Joomla registration emails?
Using any text editor open your languange file. For english, that file is: language/en-GB/en-GB.com_user
Find the constants (in all caps) for SND_MSG , SND_MSG_ACTIVATE and there you can edit the email.
For customizing the design of Joomla! system emails, get the Joomla! Email Beautifier extension.