1. Allow for a quick and easy unsubscribe for users. It should be in the form of a link that can be included in the email that says "Click here to unsubscribe" with a link to a url that automatically unsubscribes them. Trying to explain to people how to go to a topic or forum page, not knowing it they were subscribed to a topic of a forum and where to uncheck a box is cumbersome, and frustrating for the user.
2. Bring back the subscription manager. The old version had a great subscription management piece. Even though it wasn't perfect, at least it was something. Also give admins/moderators the ability to manage subscriptions for users.
The difficulty of email subscriptions is in the top 5 complaints that I get about my site.