Keep / build 4 public squares: Dudley/ So. Station; Fort Hill / Rowes Wharf; Market / Aquarium / Town Dock / Columbus Park; North End Parks / Haymarket.
Put tall buildings on the edges of these (as they already exist in Dudley and Fort Hill) with very strong pedestrian friendly edges (easy enough with so. station, quincy market, haymarket, etc.)
Fill the rest with 3-5 story, granite or brick warehouse style brick building (a la india wharf)
Build roof parks on top of these buildings and connect the rooftops and the ground-level squares with architecturally interesting pedestrian bridges / staircases / elevators.
Oh yeah, and reconnect Hanover st to cambridge st, and kill the GC garage.
Voila - an Boston style 'high line', with very intensive use (because of new low rises and high rises) with lots of neat urban rooms / public squares to explore and plenty of sun and open space up on the roof / high line for the pedestrian 'through traffic'. Plus some tax revenue.
Also - immediately kill that fucking insipid carousel.