One solution to the shunpiking issue would be to simply make it impossible by putting an AET point after every interchange.
As for traffic on local roads, personally one of the major reasons I-95 suffers from such traffic problems is that it has too many interchanges, thus encouraging many fairly local trips which have no business using a freeway to hop on for an exit or two, and creating too many merge points. The highway could stand to have its ramp count reduced. Exits 7 and 8 could be combined. Exits 10 and 11 could be combined. Exits 12, 20, 22, 26, 35, and 37 could all be removed.