Oooh, Designo interior package, eh? Nice!
With ABC, I would agree with coil springs. However, with AIRmatic, my view is different; it's fine and even desirable to leave the car stock. As long as your AIRmatic system is in good shape, i. e. behaving itself, you're good to go. Unlike ABC, AIRmatic gives you some warning before there's a "can't drive the car" problem, so you have time to order the parts and do your replacements.
Check out the brand of those air struts. If they're any of the following three--Arnott, Bilstein, or Genuine-MB (Bilstein is the OEM), then you've got good struts for sure. The pump should be a WABCO unit, which is the OEM for M-B and others. Those are the parts that tend to last a good, long while--I'm talking 135,000+ miles and such.
The rust at the bottom of those doors is, unfortunately, typical of pre-2003 W220's. The project 2000 S500 also has it. Also check inside your wheelwells, especially where the outer edge of the plastic splash shield rubs up against the wheelwell. That's a common rust point that can be arrested with proper treatment.
At about the 130,000 to 140,000 mile mark, you will be looking at a front suspension rebuild. But that's at 130K to 140K, and it applies to all cars, not just M-B's. I have done several of these, and it really isn't that hard; takes a day. Looks like you're still a good ways away from that.
"Improvements"? Well, an Android head unit to replace the factory COMAND unit is a nice touch.
and I have done this to our cars, both pre-facelift S500's like yours. Gives you the post-facelift look and, more importantly, the modern features of the Android head units, such as dash and backup cams, 4G wireless, modern GPS (including Waze), USB connectivity to devices (my "CD changer" is now a 16GB USB thumb drive), all that good stuff.
Another improvement would be new headlight assemblies. Yours are probably in good shape. My Dad's 2000 S430, always garaged and likewise pampered, came with HID reflectors. The newer HID projectors are a great improvement. The project 2000 S500 has those, and it's a huge difference on the road at night.
Other than that...I don't really see much in "improvement" that the cars need. The W220 S-class is the first of what I'd call the "modern" S-classes, and they are aging quite gracefully. I love 'em.