Howdy -
You know what they say,
"Nawth Care'lina is a valley of humility nestled between two mountains of conceit."
But North Carolina is far, far better if you want to start or finish on the ocean itself. The Outer Banks are superlicious. My pick is Ocracoke - where you can watch the sun rise over the ocean by the campground and watch the sun set over Silver Harbor on the deck of a cafe sipping a tall cool one. Just across the inlet is the ghost village of Portsmouth. There is ferry service - cheap $3 - to the mainland.
I'd start in Beaufort and head up to Cedar Island - cross to Ocracoke on the ferry - then cross again to Swan Quarter. Taking ferries and being on the ocean gives you a real sense of a beginning to the journey. Halfway between Swan Quarter and Edenton is the Somerset Plantation on Phelps Lake - great swamp country and a beautiful state park. And Edenton is a wonderful colonial town without all the bull and tourists of Williamsburg.
It really is SOOOOOO much better in NC. Far less traffic, nice camping, the ocean, ferries, swamp country. The one drawback is getting to the start. It's tricky, but you can fly into Raleigh and connect to Trailways to New Bern. I'm not sure if the bus still goes to Morehead City. Call the New Bern chamber of commerce.
As for the mountains - I also agree that the Transam route is questionable. I'd get on the Blue Ridge Parkway (avoid weekends!!!) and take it to Galax. Then catch a wee bit of the New River Trail - nice remote camping - then over to Troutdale and the Virginia Creeper Trail to Abingdon. If you are interested in this route, I'll fill you in on some incredible back roads that follow the valleys and run along the banks of the rivers.
So you'll get both Carolina and Virginny if you do this.
Best - J