Gotta agree with Stick -- Lots of overthinking and attempting to be 800 things at once (ahem... Copley Plaza...). If you're not going to enclose it with low-rise buildings to make it an actual "plaza" a la Plaza Mayor, St. Mark's Square, Piazza del Campo, etc., then why not just make it a smaller version of Boston Common -- all grass (with the exception of walking paths), with a buncha trees and a water feature or some shit?
A lot of grass and trees means its more of a park than a plaza. If you want an actual plaza here, you need programming, and for programming, you typically need typical hardscape to make it work. You can add plenty of trees and still have active spaces perhaps, but it could limit you a little.
The plaza as it is, is not optimized to have a proper mix of spaces that integrate well with each other. Enclosing it on the edges and redeveloping the JFK low-rise and thoughtfully incorporating the new development with a properly scaled plaza and promenade would be the best option, in my opinion, but seeing as we're sinking the equivalent cost of a new elementary/middle school into this, ($70m), it's going to be a while before the city wants to do anything considerable for the very long term prospects of Government Center.