I have a usability complaint/suggestion:
I spent too much time trying to figure out how to change the WordPress system emails to use the default Newsletter template. Why? Because there are 'Set as Send Default' and 'Set as System Default' options on the Manage Templates settings page. Well, hey, that sounds completely reasonable. But, that won't do it. Instead, you have to go to the System tab (NOT the System Emails tab) and select a template from the 'WordPress Related' section. I think this is needlessly confusing and, I still am left wondering what the 'Set as System Default' option actually does in the Manage Templates setting section.
By the way, speaking of the Manage Templates settings page, even after reading your tutorials I still don't fully understand when you would and wouldn't want to select the 'Use a styled, default template for newsletters and system emails' option. You select that when you DO want to use one of the templates or when you don't (and thus, some unknown system default template is used?). Really unclear.
So, I suggest you (1) make it simpler to set the defaults and (2) write a tutorial/article explaining the proper procedure.
Don't misunderstand, so far I love your product, this is just one thing that left me scratching my head. Thanks.