Please just remove the garage... and renovate the entire Bay Back Station... and open up that Trinity Pl alley and run it from Clarendon to Dartmouth.
Okay, sorry, but I'm about to go all fantasy land here...
1) Bulldoze Back Bay Station and the parking garage.
2) Construct Back Bay to provide proper ventilation, capacity, etc. Maybe even toss in [provisions for] a [fare controlled] tunnel from Back Bay to Copley, potentially allowing for basement-level retail connections.
3) In reconstructing Back Bay, extend the Southwest Corridor Park/Bikeway to Berkley St (leaving potential to extend to intersection of Arlington & Tremont, and then put bike lanes up Tremont and down Herald.
4) Extend Trinity Pl from Clarendon to Dartmouth.
5) Let them build over the SWC Park and Back Bay Station, combined with the former garage space.
6) Another, smaller parcel to build on surrounded by Trinity, Dartmouth, and Stuart.