One of the main reasons why the Downeaster goes via the Lowell Line is because of Anderson Woburn. You can overnight park and there is more convenient highway access than anything between Boston and Haverhill on the Haverhill line
The Edward Dana Bridge (over the Mystic River between Assembly and Wellington) has very different deck profiles for the rapid transit and mainline tracks. It's unlikely that the third track could handle a mainline train on the bridge.
The lower Lowell Line will always be the better route for Haverhill and intercity service. It has far fewer grade crossings, and doesn't share track with the Eastern Route.