Optimal transportation planning relies heavily on "spoke and hub" configurations. They resemble a bicycle wheel with a central hub and spokes coming out of it. This is considered optimal whether you are distributing packages (Fed Ex) or people (Delta Airlines). This keeps costs low since it ensures that all vehicles will be operating as close to capacity as possible. Exceptions are heavy traffic areas like the NYC-Washington or Tokyo-Osaka corridors which can keep planes, trains and buses full and use direct flights. For most situations, like the Bay Area, hub-spoke is optimal.
The current development of Sunnyvale is going to create the worst possible situation leading to more congestion, pollution, fuel INefficiency, and higher transportation costs all around. It will produce a lot of little mini-centers scattered around with no central transportation system connecting them in any logical way. We will become like LA, with no center and everyone commuting from everywhere to everywhere.
Here is why: consider 7 points (P1, P2, ...P7) that need connecting. If you try to connect every point directly, you need to connect P1 to each of the 6 other points, P2 to each of the 5 remaining points (not counting P1-P2 which was previously connected), etc. So you have to make 6+5+4+3+2+1 = 21 connections - roads, rail systems, bus routes, whatever. If you use a hub-spoke system, you need only 7 connections to the hub and you are done - 1/3 as many connections. If there are 9 points, 38 direct connections are needed but with only 9 spokes on the hub the ratio of connections needed goes from 1:3 to over 1:4.
Hubs are workplaces like San Francisco and San Jose. The spokes go out to living places. Create a lot of hubs because every little town likes the low maintenance high revenue workplaces and you end up with a lot of point-to-point roads and severely underused (and therefore inefficient) buses.
If everyone is driving a car you need to build and maintain 21 roads connecting mini-centers. Building, maintaining, and expanding roads is not free but it is nowhere nearly as expansive as inefficient public transportation. If you want to install a public transportation system, you need to consider the cost of running a partly empty bus, plane, or rail car. Running a bus over each of the 21 direct connections compared to the 7 hub-spoke connections is going to mean only 1/3 the ridership on each bus. A bus needs an average of 9-18 riders to be as efficient as a Toyota Prius. The average car fuel economy in the US will exceed that of the most efficient Prius within 25 years.
Of the $218 Billion (with a B) to be spent on transportation in the Bay Area over the next 25 years, 30% is to maintain roads, 65% is for public transportation, and 5% is for road expansion.