@Spoon and Stream: You're both touching on the benefits of NAVWAR... and the downsides.
The extra land at NAVWAR lets you spread the layout around for a much nicer user experience. For instance look at what it would be like arriving as a trolley passenger. At NAVWAR you'll arrive in a wide, open area directly underneath the main structure. Above, a large portal allows natural light from within the great hall to stream down into the station.
You ascend the escalators up through that portal to the grand hall, with the APM station directly above you (or alternately, with another set of escalators going back down to the APM tunnel laying in front of you).
At ITC, you arrive in a much narrower station. Although you are at ground level, with the mass of structure curved above you it feels like an underground subway station. You take an escalator up onto the first floor through a narrow portal. Around you masses of cars, buses, and taxis are disgorging their passengers.
[No rendering because it looks really boring]
The new entrants join you on a second set of escalators to rise up into the great hall which, admittedly, is just as grand as the one at NAVWAR would be. The APM station lies a fair distance away near the entrance to the hall, on the other side of a roadway (alternatively, raised on a platform just above the entrance).
For COASTER riders the dichotomy is even larger. The NAVWAR experience is virtually the same as a trolley rider, but with the ITC you arrive at Old Town Station. You know, the current station, which looks more or less the same it does today. Nearby is an APM platform. You step on and the doors close. You travel up and over the freeway before stopping in front of the great hall. It looms large in the window, so you admire it a bit before the doors close again and you continue on your way. (@spoon: connecting to the Old Town station is why the APM station is where it is instead of just to the right of the great hall. It's too much curve to send the tracks behind the ITC and back around to the ROW of PCH).
Both of these options accomplish the same mission. The time it takes the average rider to get from their chosen mode of transport to the airport is roughly the same*. The statistics are going to tell you the ridership will be roughly the same because of that. You can't quantify how many more people will use public transit if a station "feels" better, if indeed any at all do. So, is the better experience worth spending $2-3 billion extra? Or to put it another way, is it worth building the absolute best possible Grand Central instead of, say, a trolley line from downtown to SDSU via North park? I won't pretend to know the answer to that.
And then there's the outside development aspect. NAWAR blows ITC out of the water on this, with near double the potential impact area it could potentially be a second downtown. But greater development brings its own issues. That little park you see on the plans for NAVWAR, on the over side of the 5? That's from the 11 houses that have to be eminent domained because the great hall is going to block all their sunlight. One of them has already been designated a historic resource, and this is literally down the street from the HQ of Save Our Heritage Organization (SOHO), San Diego's primary historic preservation group. And with the community plan update, the Midway-Pacific Community Planning Group who made it is already angry things have progressed this far without them being consulted. They're saying the plan they so carefully crafted can't handle the central nexus of San Diego transit being plopped down right in the middle of it. Can SANDAG navigate an ardent NIMBY opposition while sticking to the Navy's tight schedule timelines? Well... there's a reason they haven't stopped studying alternatives to NAVWAR yet.
*The extra time taken by walking through the ITC's great hall is offset by it being physically closer to the airport, reducing the travel time on the APM. Similarly, the extra time taken by COASTER passengers on the APM is outweighed by the far larger number of trolley/car/taxi/bus passengers saving 2-3 minutes each because the ITC is closer to the terminals.