MIT already has aircraft designs that use 50% less fuel per seat-mile. If more of the plane is empty there is higher incentive to reduce seat mile cost especially if average seat mile revenue is lower.
Can you show me a ref to this design? (And yes, I tried to find it myself.)
I suspect it doesn't actually work for the simple reason that fuel is the number 1 expense of airlines, and a 50% reduction would be utterly enormous for them - if such a thing existed it would be in extremely high demand.