I wasn't talking technology either. I was talking about the difference between a Dana 44 front end, a Dana 50, Dana 60 and Dana Super60, and the difference between a Ford 10.25 and 10.5 rear end, as well as the engines and transmissions. The F250 used to be (in the 1980s and 1990s) based on the light duty F150. It is now based on a light/medium (kind of hybrid) duty truck. The payload may not be as high, but the components are more robust with higher capacities. For example, the Dana Super60 is MUCH stronger than the TTB/Dana 44, Dana 50 but adds weight to the vehicle (impacting the amount of payload available before reaching the GVWR), same with the stronger frame, larger brakes, diesel engines, wheels, etc.
Think of it this way, you had 3900 payload and a GVWR of 8800 lbs. So, your F250 weighed roughly 5,000 lbs empty. The current F250 weighs close to 7,000 lbs. empty. That's not just bloat, that's just about every meaningful mechanical part being stronger than the F250 was in 1980s/1990s.
You're buying a heavier truck now. Payload may have gone down, but strength is much higher, as is towing capacity. With an F250 you can only go so high with payload/GAWR anyway because non-commercial type components such as tires/wheels will be your limiting factor (not the mechanical component). So, the payload doesn't need to be 4,000 lbs if your truck weight is 3500 lbs on that axle and you have tires rated to 3,195 lbs each. At that point, you max the tires with ~2700 lbs in the bed (crew cab). The payload of an F250 regular or super cab is higher (Ford.com shows SC with a payload of up to 3,700 lbs...not that different than 3,900).
As an FYI, the listed payload is based on the weakest component as the truck is equipped from the factory (which is usually the tires). So, almost always, the manufacturer will lower the payload capacity based on that weakest link. When it comes to the current F250, all of the other components have a much higher capacity than your old F250, except the tires. So, the payload is decreased to match the tires. If the truck were equipped from the factory using higher rated tires, the capacity/payload would go up accordingly (or at least based on the next weakest component, which is likely the wheels).
ETA: if payload is the standard by which you base capacity then you're right, the current F250 isn't the truck it used to be. However, if you choose any number of other things, it's much better. For example, choose capacity to stop and the vehicle can now safely stop 10,000 lbs. as GVW or combined with an additional 15,000 lbs of trailer weight.