It's a shame you don't have much time. Depending on what it is your after, NB/NS/PEI can offer you pretty much any of it. If you wanted to hit the major sights, you'll probably want to do the confederation bridge and hang out a bit on PEI... if you're feeling adventurous and want to see some of the most beautiful land/seascapes on the planet take a drive up to cape breton and do the Cabot and Caleidh trails which would probably take you a day or two if you wanted to really dig in.
If you're into period stuff, the fortress of louisberg has been recreated to historical accuracy and offers a little slice of what life was like in the late 1700s. Pretty cool with the muskeeters marching around and whatnot.
Another nice drive is the 'lighthouse trail', on the atlantic side of nova scotia... stop in at lunenberg and see the tall ships perhaps. See the memorial for the victims of the plane crash off Peggy's Cove, or find out about aliens at Shag Harbour
If you're lucky, fall will come a tad early and colours in the high altitudes will start to come out. The best time to do the cape breton run without a doubt is early fall when everything starts to turn. Amazing pallette of tree canopies set against rugged cliffs and big seas, it's really something to behold.
5 Days really isn't enough to see a bunch. Come for a couple weeks and you can probably do a whirlwind tour.