I think this is a very exciting choice on your part! There were a few plug-ins I wanted to use that required WP-user status. While the raw awesomeness of your plug-in made me forget about those. This new direction you are taking open those options back up for me.
My only suggestion in this area would be to let an admin specify what role the user gets created with. (You may already be doing this, I would not know.) This would open up the use one of WP role extension systems to control access even further and would be a fantastic way to extend the great work you have done here. Once again I think this is a great choice, It seems to me most other “membership” systems keep their users separate like you had done in the past. I think this will put your plug-in head and shoulder above the competition and is a real selling point.
We are creating an annual member ship site. I see what you are saying but I think people shy away from automatic renewals, I know I do. I still feel a system for sending notifications on or near expiration or both really would be best… on the bright side you have almost a year to get it working