I posted this under the City Compilations section and someone else mentioned it there but one of the big differences that can't be overlooked is political leadership and how each respective region views itself.
Former mayor, Tom Bradley's leadership was very important in getting the Red line built and the commitment of Antonio Villariagosa to the current rail expansion has been very important. LA County has 10M - 11M people and LA and the surrounding counties have approximately 18M people. From what I've read (
http://www.oup.com/us/catalog/genera...E5NTE1Mzc3NA==), San Diego has long had a conflicted view of itself between a large metropolitan city and a small-town coastal area. San Diego County in recent decades has also been more politically conservative than Los Angeles County.
I also think auto congestion on LA's highways is worse than that of San Diego. LA residents have been more willing to tax themselves to pay for alternatives to highway congestion.