Okay, so I had a thought about the map (and by thought I mean dream, ha). Now, first let me say that I don't think there is another city, but hear me out. Try to reimange the map a bit having Los Santos much closer to the top left side of the map. That's still possible if the rest of the map starts going south out of view of the map snippet we saw (so north would still be north). Above it and to the west are what we've speculated, with mountains to the north and the Alamo sea to the west. But instead of extended so far north as we've been thinking, it stretches in to the southeast ending with Los Puertas (San Diego) at the very far bottom southeast portion of the map (SD is farther south and it woud be a logical cut-off point because of the Mexican border).
Sorry if this sounds completely crazy, I just thought it was an interesting idea and the map would look much more like the actual southern portion of CA.
Edit: http://www.buoyweather.com/images/regional/SD.gif -- a good example of what I mean. You can see how LS could still be on the water, there still being space above it and to the west, while it could also extend south to LP without us having seen that in the screens.