There's no reason for this to be yet another NY vs. Boston battle. (After all, we know how that will come out. Just look who won the World Series, after all!
)
I've done a little bit of research, and it seem that the MBTA's plan was/is to incent people to use the CharlieCard because it will allow the MBTA to operate more efficiently by, among other things, (1) capturing data about passenger's travel patters and (2) allowing for more efficient ways for people to pay their fares, such as by reloading your card over the internet or providing for automatic reloading when the card runs out.
I honestly don't think anyone in either Boston or NY would object to the fare difference on this basis. (It's the
exact same theory that is used in NY and Boston to provide discounted tolls for EZ Pass and FastLane users.) To the extent there's been negative publicity -- and I think it would be the same in NY -- it is that privacy advocates are not happy with the amount of personal data that the MBTA is able to capture using these cards.