Regarding the construction of a multi staged airport, with parking and security and checkin in a location separate from the actual terminals and planes... the first one/two stages would be identical regardless of whether the airport were in the ocean or in the desert.
1. you would have residents of their area of the county park and take express transit to the main security and check in hub. (residents could also drive straight to it and park if they'd prefer)
2. hub would take luggage and transport it to the airport where you would just await your check in time and get on and get going.
The only question is which of the final spots for the airplanes and main hub is preferable. This debate is on the final location of the runways and planes.
Pros- on land, land would be cheap, lack of residential noise, room for expansion, likely safe approach, good level of security
Cons- to create a route to the airport you would either have to go through the hilly east county or around the hills. It would take a long time, and track length would increase cost. Not ideal "entrance" to san diego.
Pros- great welcome to san diego, innovative and instantly world famous, high security protection, infinite room for expansion, no noise for residents, easiest approach in the world completely flat, possible environmental pluses
Cons- possibly very expensive, unproven at this scale technology, the how to get there debate, tunnel etc., possible environmental dangers