It is a big disadvantage because the expensive grade separation had to be paid out of the limited transit funds. Expensive elevators, escalators, and pedestrian ramps had to be built from transit funds. The freeway wouldn't even help traffic congestion, except for a temporary short term. Freeways increase automobile trips and increases the average automobile trip length. As with computer memory, usage increases to take advantage of any increase in capacity.
Congestion returns as before.
With more automobiles trips and an increase in miles traveled per average trip, air quality will go down. 87, enacted in 1985 by a now-defunct entity. Time is important. It would be harder to repeal after road construction is complete. I think the best approach is by getting the San Jose City Council to vote to request Caltrans to repeal their prohibition.