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An essay from In Our Path outlines how the original system lays out the backbone of the existing Los Angeles urban structure:
Unlike eastern cities, which developed transit schemes through pre-existing urban centers, Huntington's system created the basic layout of Southern California. Land development and urbanization followed the tracks. But the Big Red Cars, as the street cars were affectionately called, were never envisioned as a conduit for mass transit. Problems arose as communities the line serviced grew too rapidly and became too dispersed. The system became unprofitable to run. In addition, climate, topography, discovery of oil, and political influence favored the development of the automobile and the bus as primary means of transport.
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Now the LA basin is faced with having completed the circle: an urban form that was originally compact but then sprawled to form subregional centers based upon the highway grid overlaid on the stripped-out red line structure. The highways took suburban expansion to its extreme, and now the linkages must be re-formed, as happened in the eastern cities with public transitways between these new suburban "edge cities". The light rail system is slowly evolving into a regional public transit system of light rail, metrolink rail, bikeways, freeway lanes and buses that connect these local urban centers. Interestingly, a map of these light rail connectors mirror the original Red Car system laid down by Henry Huntington 125 years ago.
The planning for these future extensions and integration strategies by the MTA can be found here, along with a link to the 2009 Long Range Transportation Plan.
Efforts to link subregional urban centers with rail systems are fraught with politics and budget issues, as well as resistance by communities to new transit systems being imposed on their community fabric. Or even more devastating, the possibility of a small community being essentially obliterated, such as is still being thrashed out between the state and federal highway planning and the City of South Pasadena over the 710 freeway connector. This connector has been stopped for the moment as the underground connector solution is being studied, however, the objections to this have amplified in even more communities, such as La Canada Flintridge and Glendale.
Another example of the difference between idealized subregional transit connections and the reality of budgets and community concerns is the demise of the SFV East-West Rail Transit Project being developed back in 1991: an elevated monorail connecting the SVF cities with the Warner Center at Universal City. (full disclosure, I worked on it). The elevated line was selected as the favored option by the MTA with a subway concept as an alternative. Cost debates ensued, and wrangling by the County Supervisors produced further cost estimates that ultimately brought down both proposals. The Los Angeles County Transportation Commission Long Range Plan of 1992 included the SFV EW Transit Project, pending the outcome of the EIR and Public-Private Partnership initiatives.
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Because of the contentious political atmosphere around the transit concepts, the voters were unwilling to vote for Bond funding to carry them out, and thus the projects were discarded in favor of a bus sytem (the Orange Line) that was cheaper and did not involve huge public works funding. So the transit linkage picture is a complex situation in Los Angeles, which is slowly being worked out between the communities, the MTA and the local and Federal agencies. It's a long and convoluted process which unfortunately precludes the overarching public policy view of effective transit design as direct linkages to urban centers.