Soft close doors and automatic trunk were optional on '04 W220s, so I assume they were also optional on earlier models.
Airmatic was the standard suspension on all but the 12-cylinder models (S600) and the AMG versions. Automatic Body Control (ABC) was optional on all models but the 12-cylinder (S600) and AMG versions. ABC is hydraulic. Airmatic is pneumatic. ABC was less problematic than Airmatic on early models. The faults with Airmatic were corrected toward the end of the '03 MY. '04-'06 MY W220 Airmatic was mostly trouble-free. Earlier MY cars that have had the Airmatic replaced with later version struts should be relatively trouble-free, but that is a $2000 or so a corner repair, so it is uncommon. There are less expensive kits that "repair" the old gen struts.
Poorly maintained versions, no matter what MY are likely to be money pits and repair nightmares. Much of what is likely to go wrong with a W220 can be prevented with correct maintenance.
Starting with MY '04, the V-8 versions got a 7-speed transmission and all versions got DVD-based nav rather than the multiple CD-based system in earlier MYs.
General consensus is buy the latest MY you can afford, and in any event, buy '04 or later.
A rigorous PPI by a certified MB tech is essential.
That said, I have an '04 MY S430. I bought it still under factory warranty, and have put 22k miles on it in two years. It has not required any repair for any reason during that time. It averages 22 mpg in mixed driving and gets 28 mpg at a steady 80 mph. It is all the flagship Mercedes sedan should and promises to be, and I have been entirely satisfied with my decision to buy it. It was maintained as recommended by certified techs and I continue to maintain it that way.
Note the MY I own carefully--not all W220s are the same, and you would be very naive to assume they are.