It may seem a little counterintuitive, but I'm going to suggest that you take a slightly longer route from Baltimore to Burlington and take I-83 up to Harrisburg and then I-81/I-80 to East Stroudsburg to hook up with US-209 through the Delaware Water Gap, followed by I-84/I-87 up the Hudson River valley and Adirondack Park to Port Kent, NY. That is a much more relaxing and scenic drive than fighting your way up the MD/DE/NJ Turnpikes and through New York City, and if you time it right, you'll end the day with a sunset cruise across Lake Champlain on the ferry into Burlington.
US-2 is a great road across northern New England, but try to make time for either the Kancamagus Highway or the Patte Brooke Auto Tour. Hiking opportunities abound as you cross the Green, White and Longfellow Mountains. For some more sites worth considering check out the places mentioned or linked to here. Accommodations on Mount Desert Island (where Acadia National Park is located) can get a bit pricey, so consider staying in nearby Ellsworth instead. there are tons of lobster houses along the coasts of Maine and New Hampshire, and since seafood is a relatively simple food to prepare, almost any of them will provide a great experience - just watch (or ask) for where the locals eat.
Another place where you can avoid some urban areas and crowds is to substitute Cape Ann for Cape Cod. Cape Ann is north of Boston and includes the old (and current) fishing town of Gloucester as well as the 'quaint' town of Rockport. Combined with a visit to Plum Island along the northern coast of Massachusetts this would make a great alternative to the more popular Cape south of Boston, and you could avoid driving through Boston as well. Whale watching tours are available from Gloucester.
AZBuck