That is one common doubt that I actually had when I decided come here. Downtown? Pacific Beach? La Jolla?At first I did not know anybody so I stayed for a month in a homestay what I think is a good choice because you will have enough time to meet people and figure out which places do you need to be close.
For me that’s the point: be close to where you will study, work, whatever because the public transportations is not really good here. So, first of all, you should consider it.
In my case, I found my roomies at Craiglist and I can tell you that really worked, we are living together for seven months and I have no complains at all.
Maybe a second point that you should consider is the “neighborhood facilities/benefits” like PB, beyond the beach there are lots of night clubs, bars and young people living there. Downtown also have this nightlife but it is more “fancy” and business neighborhood.
Here in La Jolla I have everything that I need (grocery store, theater, shopping mall, bus, shuttle…) so again: figure out what your needs are and what you want to be close but anyway, I’m sure you will fall in love with the city.