My opinion is the JFK tower being generally good architectural form is the fact the Sudbury echoes it heavily and successfully. I don't even mind the low rise - it all just needs a really good cleaning.
My personal Government Center bugbear is Center Plaza. We've talked about all the other under activated plazas - Hurley/Lindemann, City Hall Plaza, but Center Plaza is architectural ennui that commits the unique sin of blocking off the John Adams Courthouse. Opening up Pemberton Square and reframing it would do a world of good around here.