When traveling, I have always felt it is better to really see a smaller area, rather than a quick drive by for the sake of saying you have been there. What are your interests? If you enjoy hiking, I would consider doing the Cape Breton Trail and spending 2 or 3 nights along the trail to provide time for some of the wonderful hikes.
Peggy's Cove and Lunenburg are also worth a visit, albeit rather touristy, but worth the experience. We also have spent time doing Digby Neck and whale watching while in the area. As suggested, Annapolis Valley is also nice.
With the limited time you have available, I suggest you study the Doers and Dreamers Guide and pick the area(s) that is of most interest to you.