So here's an answer to all of that.. and more. With the Email Beautifier, making your Joomla emails look nicer is as simple as A-B-C. Email Beautifier catches all* emails going from your Joomla site, wraps an awesome template around them & sends them on their way. For extensions that have their own Email templates like AcyMailing, Invitex or J!MailAlerts, you can simply choose to skip their transformation in the configuration.
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* Note that Email Beautifier can only catch those emails that use Joomla's Native Email Class for sending emails. This is the case with most Joomla Extensions. Some extensions like Community Builder are known to use their own Library. So emails generated by such extensions cannot be beautified.