This is a most basic requirement of any pop-up solution:
1. Hide pop-up on selected pages/posts
2. Display pop-ups continuosly on rest of pages
3. Hide pop-ups once subscription is achieved. This can be based on ip address and cookies both.
4. Hide pop-up for loggedin users
These 3 simple actions can make a very good pop-up solution i think. This is clearly missing in thenewsletterplugin and as a result it has become very difficult to give a good user experience.