Zone based fares make sense on the Metro because it's coverage area mimics commuter rail. I'm not sure how much sense they make on the T. I could see a discount incentive for people that don't go into the heaviest areas, (Commuting from say Alewife to Harvard) but I don't think we should start discounting a trip from Park to Copley or Charles MGH to South Station. That's going to put more people into the busiest part of the system.
What some cities do, e.g. Berlin, or Paris until its ongoing transition to single-zone fares regionwide*, is have the inner zone comprise only city center, but then only sell tickets for at least 2 zones. In Berlin, this is the simplest, with 3 zones: A is inner Berlin, B is outer Berlin, C is the suburbs served by the S-Bahn. The transport association sells AB and BC tickets, which cost about the same, and ABC tickets, which are more expensive. This doesn't cheapen the equivalent of Alewife-Harvard tickets, but does cheapen the equivalent of Norwood-Forest Hills, Wellesley-Allston, and Salem-Chelsea tickets.
The A/B zone boundary is set at the Ringbahn, so the Boston equivalent would be to set it at the Urban Ring. In Berlin the Ringbahn itself is in Zone A, but I'd recommend that Boston set the Urban Ring itself in Zone B, since the congestion in Boston is more localized to downtown and Back Bay. Berlin sets the B/C zone boundary at city limits, which are much looser than in Boston; for Boston, the rough equivalent is the outer limits of the cities served by the subway and frequent local buses.
Of course, since Boston commuter rail extends far out, there would have to be multiple concentric zones beyond Zone C, like Paris's zones 1-6, or Berlin's farther-out zones on the Regionalbahn, which aren't part of the A/B/C system. There would also be non-concentric zones for independent cities like Worcester and New Bedford, and of course a separate zonal system for Rhode Island. But within the zone system, fares would be mode-neutral, with unlimited free transfers: a Downtown Boston-Worcester ticket is automatically also a ticket on transit within Worcester and Boston.
*In Paris, most suburbs are much poorer than the city; one suburban department, Seine-St.-Denis, is the poorest department in France, while Paris itself is either the richest or one of the richest. The zoneless regional fares were passed by the Socialist-Green coalition as an equity plan. In Boston, I would recommend against it, since the poverty is concentrated in the city and in inner suburbs that would be part of the city zone.
