The segment from Fort Washington Park, under the BU Bridge and then linking to the Esplanade and Comm Ave is my highest priority segment since it creates a lot of neighborhood and regional connections that are currently stressful or impossible. Linking Cambridge, Allston, and Brookline into the PDW path and pulling bicyclists off of the BU bridge mess would be huge.
The segment from the future Somerville Community Path down to Binney Street would be my next priority due to a general lack of low stress N/S routes there, but doing a true bicycle boulevard treatment on Sixth Street could push off a need for that segment of the Grand Junction Path.
You’re right, the bit in the middle isn’t that important for regional bike travel. The Vassar Street protected bike lanes could use some minor repair work, some modernization, and a redesigned intersection at Mass Ave. But really they're fine and provide a higher level of service for bicyclists than the Grand Junction path would. The multiuse path through MIT is still a good project and will be great for walking around the campus and tootling around by bike.
But if it costs ~ $700,000 to build the 700 feet from Broadway to Main, then ideally that would be the last segment that gets built.