The autopilot can definitely have an effect on how smooth the flying feels, depending on how autothrottle and altitude hold control loops are implemented.
There are parts of the flight where hand flying is allowed, but those are the parts closer to the ground (or on very short hops where the cruise altitude is significantly lower than usual).
Airline pilots routinely do takeoffs/departures/approaches/landings by hand to practice their skills, but not cruise. See this Airbus doc: https://safetyfirst.airbus.com/high-altitude-manual-flying/
Cyclists generally prefer carbon fiber over aluminum because the former is smoother than the latter. 787 is carbon fiber, A380 is a fiberglass/aluminum composite. I wonder if that's why the 787 is smooth.
I'm not an expert on planes but I'm not aware of another commercial airliner that's carbon fiber.
Sorry for the highly technical terms but I agree it is unique to the A380.
Apart from this they comfortable to travel and sleep on.