Create your own custom message templates (not just override the current ones).
For example we wanted to send out a customised new user email to users we were bulk importing, and the only way to send a customised email was to override the generic template, import the users and then add back the generic text.
This will be very beneficial when you wish to have separate 'domains' such as an internal domain for regular users, and an external 'domain' for external users. Messaging is very different between these domains. There is already significant differentiation between internal and eCommerce domains, so adding in unique messaging for discreet groups, or whole 'domains' will be greatly beneficial.