If I buy a paper subscription, I should get the digital subscription "with it".
If I get the digital subscription "only", it should be at a slight discount from paper (to account for reduced overhead costs)
Both deliveries should have basically the same content, but with a digital subscription giving you some better search/link tools, access to archives, etc. Possibly some space for "breaking news", and feedback.
Both paper & digital deliveries should have the same ads - keep it simple. Advertisers buy ads to target readers, and it doesn't matter if the readers are looking at a digital or print copy.
Doing something fancy with ads is going to mess with the layout & presentation of these publications - I'd be surprised if it comes out looking OK.
The main problem appears to me to be someone like apple, trying to get a large cut of the revenue, and breaking this fragile model. Is apple really providing enough service to justify a 30% cut? I like apple, but I think not...