Or we could write the Silver Line off as a failed experiment and work on getting proper light rail service from South Station to the Airport?
We could also do an AirTrain! ...well, actually, we probably couldn't do an AirTrain. Is it possible to bridge over the harbor or does that have to be a tunnel?
Direct rail to the airport was deemed impossible when they cut the third transit bore out of the Ted Tunnel design to save money (you know...because they were all about reining in Big Dig cost back then). It's commonly stated that you can't mix light rail and interstate highways, but in the fine print that's not actually specified. And the Ted is exempted from Interstate highway design standards like all underwater tunnels that can only be built with tight clearances. So, yes, you could technically run an LRV through the tunnel pavement. It could even be traffic-separated on both ends of the tunnel until it hits the true precast underwater tunnel segment for the only mixed-traffic running. The under-land approaches have full-size shoulders and the concrete walkways on the side that are wide enough to fit track. Tunnel ventilation is beyond spec to mitigate explosion risk from leaking gas and an arc from the overhead (the other thing planners would clutch their pearls at), and at that short a distance an off-wire LRV like the Kinki AmeriTram can cruise through the mid-segment and pick up the overhead at each portal. Functionally it's not really any different than the current dual-mode experience, and the oft-cited "well, a bus can change lanes around an obstruction" becomes a miniscule factor in a tunnel where lane changes are prohibited and moving around obstructions is hard enough for the cars. There's such limited space for that a vehicle probably only gets one shot end-to-end to actually change lanes. So put 1-2 turnouts somewhere in the middle where a short runaround track segment can act as a lane switch.
But...seriously, is anyone ever going to consider that? They'd be terrified to. And I'm fairly sure sure it would make any difference over the BRT mode because a high-speed tunnel is a fixed guideway all the same. What they need to do is grade-separate on each end of the tunnel. Eliminate @#$% D St. crossing before it kills someone and give the buses a dedicated ramp in and out of the tunnel. Then you've got "true-true" BRT with the requisite dedicated ROW everywhere except where physically impossible for any mode, and same trip times. This is absolutely the correct application of BRT, in the place where high-density rail is impractical. It's the rest of the SL and hit-sandwich Phase III that don't pass the smell test, and the Transitway that screams out for dual LRT+BRT use.
In retrospect, Big Dig planners probably would've and should've gone for the third Ted transit bore if they knew what "cost control" was really going to entail for that adventure. The Ted was one of the few portions of the project that didn't become a total unhinged corruption pit. Mainly because it was the first piece of all to get built, before the political-criminal enterprise got its claws in all. But that compromise seemed sensible at the time, and rail-to-Airport-from-South-Station is not so high a priority to dredge open the harbor again. Not when the Blue Line is a reliable-enough #2 route, and not when Phase III of the Urban Ring *ostensibly* is direct-rail overland on an existing rail ROW for a third link. After its own BRT/Phase II interlude.
What I think they should do 2 dozen years from now when Logan's inevitably up for its next new radical Central Parking/terminal makeover is to put an El or grade-separated ROW grafted onto the 2nd level snaking around Central Parking as a true Airport transit loop. And like the Transitway
should be have it done as pavement + buried rails with shared overhead so trolleys coming off the UR via Chelsea and BRT coming off the Ted can share it together. Without either needing to crawl in terminal traffic.