I'd guess that one reason the Marathon route wasn't chosen to go through historic Concord, Lexington, Arlington, etc. is that it would interfere with those towns' various Patriots Day re-enactments and celebrations.

That said, the route does pass its share of interesting local sites -- Lake Cochituate, Natick town common, Wellesley College, Boston College, Chestnut Hill Reservoir, and Fenway Park.