We've had an S P85 (VIN 3xxx) since early 2013 and our new S 100D since May.
Navigation/real-time traffic: I had real-time traffic in my previous 2007 Lexus, but it was only for the major highways in major cities. The Tesla routing has real-time traffic data from Google for all roads, and tries to adjust the route for optimum timing, but some of the routing can be pretty convoluted, so if you see an odd routing on surface streets, you might want to ignore the advice, or wait a few minutes to see if the route changes again to something that makes more sense. One feature that my 2007 Lexus had was pop-up warnings of traffic issues on the route. When there was a problem, the Lexus system would ask if I wanted to re-route around the problem. With the Tesla NAV, there aren't any pop-up warnings, the route is changed automatically (and sometimes frequently).
All glass roof: Our cars have the sunroof. Our S 100D is quieter than the S P85, the biggest difference is the tire noise, with the 100D coming with the new sound deadening tires. Don't believe the sunroof is the source of much noise inside the cabin.
Air suspension: We have the air suspension upgrade on both cars. The low-high-very high settings adjust the height - not the comfort level. At highway speeds, you can lower the car, which may provide a small improvement in efficiency and handling. At slower speeds, you can adjust to high or very high to get increased clearance over objects, such as speed bumps or curbs. And with the geofencing feature, once you've set the suspension to high or very high at a location (like a parking lot or driveway), the car should remember that and change the height when approaching the area in the future.
Scheduling pre-conditioning of the cabin: For us, this is an issue only when the car is parked outside. We use the smartphone app to start the climate system when we're approaching the car. If it's hot outside, we'll also use the app to "vent" the sunroof - which also helps to cool the car down. After a few minutes, the cabin is comfortable. This is so easy to do - we haven't found a need to schedule the pre-conditioning.