It should be a no-brainer that a sea-wall of some sort will have to be constructed. I can't imagine the economic cost of a major retreat out of a city even modestly sized like Boston - that's talking about hundreds of billions of dollars of real-estate being abandoned/lost.
Ugh - I hate the argument that the general population has to back wealthy waterfront landowners' poor investments... Privatize gains, socialize losses. Gross.
Major infrastructure investment happens only after decades of planning, or one big disaster - so let's look at this from a "next big wave" scenario since it's easier. What would happen after 1 big storm?
1. Downtown gets flooded, and drains away, because it's been designed to do that for 200 years. No change.
2. Charles River Dam gets overrun, and all of cambridgeport, MIT, and Back Bay get water they've never seen before. All of the new Beacon Yards is flooded. Massive disaster and lots of structural issues since they're all built on fill anyway. Lots of political capital - definitely is getting rebuilt.
3. Water shoots up the Fort Point channel and floods the south end - drains out pretty quickly but stops South End development.
4. Mystic River Amelia Earhart dam gets overrun, and seawater floods Assembly then all the way up the Mystic and Alewife to Fresh Pond, which is now back to being a Marsh and takes months to get rid of water.
5. Seaport is flooded, and we test all these new "flood mitigation" structural decisions.
Seawalls might be a reality, but not across the harbor. Much more likely and manageable across the Charles and Mystic where storm surge is a much greater threat to larger communities instead of individual buildings.
My prediction? I see major commercial TOD growth in Harvard/Porter/Davis on Red, Sullivan and Malden Center on Orange. There will almost definitely be growth in Roxbury, and look to Chelsea Center getting an influx of development over the next 50 years, both likely rail connections. Seaport is seen as a great mistake of Boston development history.