Shocks - Generally aftermarket Bilstein's are considered a "superior" shock and many users in other Class C and Class A coaches report them to provide a more civilized ride than the stock shock absorbers installed by the factory. But I don't know what Freightliner put on my unit to start with.
Regarding the mods, you could install air seats if you had the money and could source the seats and other parts; but air brakes are a whole other matter. That would be a MAJOR change involving hundreds of items to be swapped out. One "goof" and you have an unsafe vehicle. The cost to make such a change would likely be in the tens of thousands of dollars, if you could even do it without swapping the whole front and rear axle assemblies out.
When I first saw information about Jayco's change to air brakes for the Seneca I asked on the other threads what difference someone who may have driven an old (hydraulic) coach versus new (air) brake-equipped coach thought it made. I have not seen any feedback yet. My 2014 Seneca has hydraulic brakes and with 5,000+ miles behind the wheel I am very pleased with my brakes. As a retired career firefighter I also drove many trucks with air brakes. They also stopped very well, but not any "better" and usually had longer stopping differences. But that could be attributed to their greater weight. My Seneca with toad can only (legally) weigh a maximum of 33,000 lbs, some fire trucks I drove approached 70,000. Obviously takes more to stop that amount. And very importantly, you do need to be educated to properly drive with air brakes. What you don't know can hurt you. You can learn that information by getting a CDL, but in many (most) states driving a RV does not require a CDL. But I would strongly encourage anyone who drives an air-brake equipped coach to seek out that training before they take any trips in their new coach.