It's true that a lot of the coast is privately owned, but keep in mind that anything below the high tide line—even on so-called "private property"—is public domain. That being said, there are loads of wonderful places to explore. Mount Desert Island alone should keep you pretty busy. Definitely buy the DeLorme Maine Atlas; very useful for back roads and points of interest.
Although I've never taken them, there are excursion boats that go out to the islands in Frenchman's Bay.
There's a lot to explore further up the coast ("Down East"). The Schoodic Peninsula—the next peninsula going east—is part of Acadia. Further down east, there's the Jonesport area with some nice nature preserves, also Petite Manan and Grand Manan Islands. Check out
http://www.fws.gov/northeast/mainecoastal/Just west of Mount Desert is a wonderful peninsula-cum-islands with many small towns, real Down East feel, lots to shoot. Stonington is my favorite, Blue Hill is more artsy. A spectacular view of the whole Penobscot Bay from a high pull-off on Rt....175, I think, but I could be wrong. And there's a beautiful little Nature Conservancy plot called "Barred Island" on the western side of Deer Isle near Stonington and the hamlet of Sunset (gotta hunt around a bit for it, but it's shown on the Delorme map).
Bar Harbor can be a tourist trap. It won't be so bad in October, but there will still be plenty of people about, especially if the fall colors are good.
Have fun!
Merrill