The first would to be able to have a rotation of popups, so that I can have a lineup of 5 popups for all visitors from http://www.somewebsite.com, that way if they are coming in twice in 2 days they aren't going to see the same popup twice and while they may have closed the first one they could open the second
The next suggestion, which would tie in with the first is popup statistics. I figured this would be an easy one to implement as it would just have to ping a table saying "I've been activated" so that users could see how many times over the past day , week or month the popup has been activated... Now taking this one step further and really getting at the heart of what would make this powerful is if you could correlate this with click-through stats. This way you can setup 5 popups in rotation and quickly deduce which one of those has the highest CTR rate. Very quickly you have a powerful a/b testing system in place that would be invaluable for users.