Maybe parking on the roof of one of the downtown structures to get a bit of a view? That parking lot across from Petco might let you get views of downtown and Petco, the convention center, or maybe even the Coronado Bridge into the background, maybe? And there's that parking lot at the back of Geisel Library at UCSD that might let you get "the spaceship" into the back of a shot.
Oh. Duh.
Mt. Soledad. Try that. You might have to circle a couple times to find a good spot to park the car, and it'll be a pain dodging the cars going round the monument, but it's got possibilities.