Yeah, the mediocre Silver Line (which has only become a more obvious "compromise" as the Seaport area has developed). As I understand it, there was also "supposed" to be a new better connection between North Station and South Station which never happened.
Though I shouldn't complain too much. Not that I go into the city a lot but the public transit system, including commuter rail, is pretty good by US standards overall for all its problems.
And parking at Logan is such a mess that I just get driven, expensive as it is. Even economy parking is expensive and it's practically in another state.
In some parallel universe Boston is yukking it up with a high frequency train from Roxbury to the South End (along the original elevated Orange line route) to South Station to Seaport to the Airport and I hate them for it. I just know they demolished Central Parking at Logan and built a gleaming rail terminal in its place.