The Blue Hill Peninsula is gorgeous. There are a handful of very sweet towns/villages, each with it's own feel. Castine is refined with its rows of lovingly restored white clapboard federal houses. Stonington at the southernmost tip is rustic with a classic/authenic lobstering harbor, one of the most photogenic harbors in the state and a favorite of kayakers. (Go to this site and click the fourth thumbnail down. That's sunrise at the Stongington Harbor.) Deer Isle is well known for its art colony. Blue Hill has beautiful homes, nice restaurants. Blueberry barrens dot the whole peninsula and offer lovely views out over Penobscot Bay. Brooklin is tiny, but has always held a special place in my heart because of EB White's having lived there.
If you want to rent a house for a week, you'll find so much more for your money on the BHP than in the Acadia Region. Try A Better View, see http://www.abetterviewrental.com/
As pretty as Brooklin is, it is teeny and I think I'd send you to Stonington if you plan to visit for several days. There is more to do there--but not as much as Acadia, but there is a strip of downtown about two blocks long with a few stores, ice cream shop, grocery, active waterfront, etc., lobster pounds nearby, restaurants, etc.
If you like the Deer Isle Stonington area, but what a resort feel, try Goose Cove Lodge, http://www.goosecovelodge.com/
If you want more high end, try Castine, where there are several very nice small hotels/B&Bs, tennis, golf, waterfront, historic tours.
You can make day trips to Acadia from the Blue Hill Peninsula, but the farther you go down the Peninsula, the farther it is to Acadia.
My extended family came to visit for a week last summer I actually wanted to rent in Stonington, but they needed lots of stuff going on and they outvoted me and chose Acadia.
However, if you really do prefer a quieter pace and are able to entertain yourselves, and don't care for the crowds of Bar Harbor, then you could have a fabulous vacation with a base in Stonington. Rent kayaks and explore the lovely islands off of Stonington. Take the Isle au Haut cruise one day.
There are so many spectacular parts of Maine, it's really hard to say that one is better/prettier than another, but Stonington is a true gem.
See if you can find a copy of "Maine: The Seasons" http://www.tlesterphotography.com/bio.htm That photographer is based in Deer Isle and many of the photos in that book are of Stonington/Deer Isle.