T39 is probably the one I disagree with the most. Like you said it's looong. For riders on the Forest Hills - Heath Street stretch (which is the whole reason the "old" 39 existed in the first place), I don't think it's a net gain in service. It's basically a forced transfer to the E or backtrack to Forest Hills to get the Orange to get to Back Bay or Downtown, whereas the existing service allowed riders to take any Green train to Copley and transfer. In a vacuum it makes sense, but given the history of the route I don't think this one will fly.
It's certainly a provocative proposal (or as HenryAlan put it, revolutionary). Given how long it is, I almost feel like there must be something they are assuming to improve reliability -- bus lanes, TSP?
Doing some math, just to sanity check: right now (a bit before 4pm on a Monday), Google say the 39 takes 24 minutes from Forest Hills to LMA. Then the 47 takes 21 minutes from LMA to Central. The 91 takes 6 minutes from Central to Union, and the 87 takes 9 minutes from Union to the Porter area. So that's an hour on the dot, though admittedly not during the height of rush hour. Google estimates driving that route to be 52 minutes right now, but if I push the departure closer to 5pm, the estimate goes as high as 1h20m -- and that's for driving.
So, I think there would be challenges to overcome from a reliability perspective, but I'm trying to remain open-minded.
Setting aside north-of-the-Charles for a second, I'm slightly less pessimistic about rerouting through LMA;
a lot of 39 riders are going to Longwood itself. Though you are right, it is a notable loss of a one-seat ride, which didn't register with me on my first read-through.
One alternative, if they want to keep the one-seat ride across the Charles, would be to stay on Huntington until Mass Ave and then head north from there. Terminate at Kendall or Central or maybe through-run, I don't know. But you'd maintain a one-seat ride pretty close to the Pru, a short walking transfer to the Orange Line, and equal connectivity to the Green Line (all 4 branches via Symphony and Hynes). You'd also be spending more time on Huntington and Mass Ave, both wide enough to be optimistic for bus lanes.
At the same time, you could keep a "T47" that runs Porter-Union-Central-BU Bridge-LMA-Nubian/Ruggles -- or even double up the T47 and T39 along South Huntington.
But I agree with
@HenryAlan -- if they can make the proposed corridor viable, that would be a remarkable service.