The central problem here is a fallacy that Michelle Wu and others are spreading that fare increases must be tied to improving service... why? The MBTA talks a big game about their "customers" as they should, but at the end of the day public transit is not a business, it's a social service. Your users aren't customers, they're partners, and we collectively fund transit in order to gain a collective benefit. [Note - transit CAN be a business in cases where you've contracted it out, as the T has to Keolis on Commuter Rail, but that doen't apply here].
This attitude of "why do you ask us to pay when you aren't giving us anything in return?" is silly. The MBTA is giving you transit. If the increasing cost of providing that transit requires that you contribute more, that's entirely appropriate.
FWIW, as Steve Poftak pointed out in the Globe the largest source of the MBTA's funding is a Statewide sales tax. I believe that fares are third, also behind Federal funding generated from the Federal gas tax. On the whole, MBTA riders are already receiving a spectacular subsidy from Massachusetts residents who either choose not to use it or who don't live in the service area. I think that's a good and necessary thing, but the whining from riders when they're asked to pay any share at all of the cost of their transportation is grating.
Making transit free for people who need it to be free is a great idea that's entirely in keeping with the concept of public transportation - being able to move freely should be a basic right that government supports. However, the share of people riding the T daily who need it to be free is not 100%, or even 50% (or probably even 30%). I have no sympathy for the person complaining about a $90 pass when they can and should pay $300.