Welcome to the realities of buying a home in San Diego in 2015.
As a native who purchased property here a long time ago, and who has also lived elsewhere, I agree with many of your comments concerning the choices you have available to you at this point in time.
A million doesn’t go as far as it used to around here, so, you will most likely have to decide what you can live with and what you can’t, based upon your financial situation, schools, access to work, etc. There’s a lot of give and take in CA housing today, so be prepared to be flexible.