You're replacing it with a worse curve AND a steeper grade to meet the Orange Line and follow its tunnels - assuming you even can follow the Orange Line (and I don't think you can.)
I guess you pick up 'Central Station' under DTX/State, which might inspire those two stations to be renovated, or it might just result in an even more confusing warren of tunnels under downtown.
Fairmount, Plymouth/Kingston, Middleboro/Lakeville and Greenbush all have no way of accessing Back Bay without a time-expensive reverse move, and assuming your new portal closes off access to the curve, they have no way of accessing Back Bay period. And, with Fairmount stub-ended like that, kiss RER-style service inside of 128 (Readville-Woburn) goodbye.
Oh, and you've also rendered the Southampton Yards totally inaccessible to Amtrak.