I'm new to this discussion (and judging by the date stamps on the posts a page back, very late to the discussion), but here's what I'd do.
I'd knock down all of the toll booths on the Pike, and replace them with
Open road tolling stations. Cash will no longer be accepted anywhere on the Pike - if you don't have a transponder already, don't worry! Automatic number plate recognition can also be used to mail you the bill for your toll, a system already in use in Florida (where it's known as TOLL-BY-PLATE. Yes, with the caps.) You will, of course, be charged additionally for the service and as an incentive to pick up a transponder.
After a few months to show that yes, this system works a whole hell of a lot better than the tool booths we've got now (seriously. The most annoying thing about fast lane is slowing down to 15 mph to go through it, right? Not so here!) and doesn't even require us to staff toll booths, I'd have Open Road Tolling stations added to every entrance and exit to the Big Dig tunnels of 93. You would pay once to get on, and once more to get off.
I'd also hike individual ride fares, but leave the monthly passes alone as an incentive to buy. I'd implement the technology that we know the MBTA has already to let them load 1-day daily passes onto a CharlieCard at any ticket vending machine in any given station, just like the monthly passes can be and are. (The 7-day weekly pass would either be discontinued, or become impossible to buy on either a CharlieTicket or CharlieCard except through pass offices, as the trade-off for it being much cheaper than seven 1-day passes.) As long as we're talking about the CharlieCard, make it possible to load commuter rail monthly passes onto the CharlieCard as well.
Bus services will be slashed (including and especially the Silver Line. It comes back as a light rail or it doesn't come back at all), but commuter rail and subway services will be increased in exchange. Run new commuter rail lines out to the folks in Western Mass., and charge everything west of Worcester as a Zone 9 (and beyond) stop. (That last part is probably just my annoyance as a southern Rhode Island resident with the fact that the only Zone 9 station in existence is T.F. Green, and the commuter rail zone fare map posted at Back Bay seems to hint that Wickford Junction will become the first and only Zone 10 stop.) Maybe run new subway lines or subway branches to replace some of the slashed bus service as well.
Yes, it's dramatic and expensive, but I believe that you need to spend money to make money. Ultimately, the huge initial cost of doing these things will be quickly offset by increased ridership and new revenue from tolling the Big Dig.