Just to be explicitly clear as to what MassDOT is trying to pull off here: a new station must be constructed at the Convention Center where Summer St crosses the Haul Road, trains must proceed across the Cypher St grade crossing (which needs to be fully upgraded), trains will then proceed across diamonds in one of the few double track sections of the Old Colony line, proceed across two (at least) of the busiest tracks in the entire Southampton facility, cross the tracks of the Fairmount Line which the MBTA/MassDOT hope to get 10 minute headways on, go around the not-so-gentle curve of Widdett Circle, merge back into Fairmount/Old Colony traffic in approaching the Cove Wye, make it across the three most congested train tracks in the entire state, and then dwell for reverse on of the Worcester Line tracks at Back Bay (a line which needs improved schedules and more frequent service).
And we're doing this why? Because the Silver Bus is deemed insufficient before they're even running the maximum volume of buses. (Another reason I would like to call the Big Dig the gift that keeps on giving - years later, we're stilling looking for multi-million dollar band aids and half assed alternatives)
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Now tell me, does this not sound more appealing in every aspect other than aggregate cost?: the Piers Transitway currently ends at roughly Atlantic & Essex. Pull South Station's Tracks 1 & 2 out of service (preferably after expansion is completed), cut and cover a tunnel down to Cove Interlocking, and then the trickiest non-optional part is to dive under the I-90 tunnel. Once you clear that, there's two options: cut and cover the Worcester Line leads, the Mass Pike eastbound, or partially both (to reduce impact on either). Keep cutting and covering until you reach Back Bay Station, at which point you end the line if you wish. But here's where the fun part comes in -- opportunities! At this point, you can convert SL2 to light rail, then you can optionally bore just one block to the Huntington Ave subway, and if you do all that you could even reactivate the abandoned Tremont St tunnel which ends a block away from your new cut-and-cover under the intersection of Arlington & Tremont. This means you eliminate Copley Junction and improve the central subway of the Green Line. If there were a return to the Arborway, you could have two lines: Heath-Union Sq (Somerville) and Arborway-Seaport. SL1 could continue to loop at South Station. SL4 and SL5 could be converted and utilize the reactivated Tremont tunnel.
Now, in terms of total cost, is it more? You bet it is. A tunnel from South Station to Back Bay isn't cheap - but it sure as hell is the cheapest tunnel in terms of per mile cost in comparison to any other possible tunnel in this city! The benefits have the potential to be enormous if you take the full package and improve the entire Green Line with it. It also means the Piers Transitway wasn't a waste if we use it to it's full potential. The cost of a DMU shuttle from BCEC to Back Bay is not just procurement and track upgrades -- it is also the cost of pissing away the Piers Transitway's potential capacity. And that tunnel did NOT come cheap.