Get rid of the roads in the center except for the bus lanes. Make Plaza st 2 lanes wide right lane for turns only and left for straight. This means eliminating parking from the circle on at least one side. Restore the plaza st to its oval shap at the south end. at Union street they need to make a right turn from plaza st and move the crosswalks away from the intersections so cars are better able enter plaza st.

This way there will only need 4 traffic lights if at all, at flatbush, union, eastern parkway and Vanderbilt. Traffic will be heavy but constantly flowing so better then it is right now.

Remove all car traffic from the middle, only bus and bike. Remove the bike lane from Plaza St E & W, possibly the parking too. Make it two lanes of traffic where right lane must turn right.

West bound Eastern Parkway merges to single lane before hitting Plaza St E and is forced to turn right onto Plaza St E. Force south bound traffic on Vanderbilt and Flatbush into a single lane before their turns too.

The lights could probably be timed to send Flatbush traffic around almost non-stop.

That whole intersection feels like it would do great as a tunnel