Did you already buy your ticket? If not, have you looked at flying into Manchester, NH, or Portland, ME, instead? Renting a car at either of them should be cheaper than at Logan, potentially offsetting a higher ticket price.

If you fly into Boston, it should be feasible to stop at Nubble Light/Cape Neddick on the way to Kennebunkport. Don't know how bad traffic might be, but I would suspect it will not be so bad you couldn't take Route 1.

Be sure to check out Spring Point Light and Bug Light in Portland as well.

http://gonewengland.about.com/od/melighthouses/ht/htmelighthouses.htm

It's not a lighthouse, although it looks like one, but the Portland Observatory is fun to visit, too.

http://portlandlandmarks.org/observatory/

Traffic won't be bad in June, it doesn't really pick up or get bothersome until nearly July...if anything there might be a short stretch of route 1 near Ogunquit that is bothersome but nothing worth trying to detour. HOWEVER...route 1 is not the best route between Cape Neddick and Ogunquit, the shore road has some breathtaking views. I think the views are actually better coming south in the other direction however, so you might want to save NubbleLight/Neddick for your Saturday drive south. Kennebunkport, to Ogunquit, then left after the town square onto Shore Road (Route 1 does not hug the coast). Matter of fact after Cape Neddick you can continue to hug the shore all the way to Kittery for some more great, but curvy driving. Then hook up with 95 at Portsmouth.

Brown's Ice Cream is a must-stop near Nubble Light. Try the Grapenut and the Indian Pudding ice creams if you want the real New-England experience.

Cupcake lover? Scratch Bakery in South Portland on the way out to Two Lights is a must. Oh but then there's Beach Pea baking in Kittery that would also wet your whistle...

On Friday, I think I would head for L.L. Bean first, before the weekend traffic picks up, shopping crowds, etc. Then backtrack to Portland and Cape Elizabeth. If you've got time to kill forget the freeway and head back to Kennebunkport on Route 1 down through Saco to Route 9 around Biddeford Pool and Cape Porpoise...this is sort of the slow coastal route back to Kennebunkport.

I would forget Route 1 - until perhaps you get to Maine. Through most of MA and NH it is strip malls and big box stores - not the romantic ideas of Route 1 from the past. There is a short stretch in northern MA where there are houses and a few cows - but also traffic lights.

A frequent piece of advice to avoid renting car at major airport - I rarely find it worth the hassle and sometimes higher cost. Doing a fast check, you would save $40-50 by renting at MHT, but it would be almost $100 more to rent in Portland (Maine has a high sales tax on everything). That plus it is much less likely you could find good flight connections into either of these airports. (We live 25 miles from Logan and about 40 miles from MHT - but about equal travel time - it rarely makes sense for us to fly to/from MHT for either time or money)

When you go to Two Lights, there is a nice (casual) place to get lobster overlooking the rocky shore.

Try to fit in a harbor cruise of Casco Bay. We did the mailboat cruise last June. A little narration, mostly just scenery but very enjoyable. The morning cruise has a lot of "commuters" who are work on one of the islands. The island kids commute to Portland high school too.

Thanks everybody for your replies and very helpful comments. I appreciate all of you.
Cranachin, I have already bought my ticket. It substantially cheaper to fly into Logan, plus it's nonstop. Portland or Manchester would eat up the whole day making a connection. It is crazy indeed how expensive it is to rent a car at Logan. Half the total is taxes and fees! It's the the worst of any city I've ever visited ever!
Joe, I will be sure to stop in at those treat places!