Well, none of this is actually going to happen, so it's a matter of what
should happen. The Tobin, for all its magestic height and presence, doesn't actually bridge much of a gap. The Mystic at that point is about 1,400 across, not much different than the Alford Street Bridge or other forgettable ones around. The Sumner, Callahan, and Ted Williams tunnels all traverse much greater channels. The reason the Tobin is so enormous is that it needs to get high enough to clear the shipping channel. Overbuilding another bridge there makes the same amount of sense as building one from the Seaport to the Airport did: none. Not to mention that if you wanted to put rail over the bridge you'd need even longer grades and shallow approaches (the old "why can't you run the Red Line down the median of Route 2" problem).
Also, The Secretary has made it her first order of business to envision dumping a tall bridge with bus lanes, so I don't think she's looking for a vision for another, on the same alignment.
Taking into account that the rail may need to tunnel alongside the highway, here's my second attempt at a concept. New twist this time: incorporate Route 16. Rebuild the Mill Creek interchange between RB Parkway and Route 1 to merge the Parkway in instead of crossing over. Downgrade Route 16 through Everett to a 4-lane multimodal boulevard (Massachusetts has no Route 16A at present, so I used a shield from Prince Edward Island). Cut Sweetser Circle down to size since the 16/99 intersection is now closer to the casino in no-one's land.
North of the Mystic, the highway doesn't even need to be tunneled - it could be in a trench. As in Allston, much cheaper to trench (or even build at-grade with sound walls) than to have a viaduct, particularly in life cycle costs.
I still prefer the T (which I've colored blue here but probably would still be the Orange Line) to take the current US-1 alignment to this one, but I'm surrendering to Van's logic.
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