I don’t think it is particularly unusual for similarly built bikes to feel slightly different. But in this case, the bikes are not even identical, so I would expect to notice at least slight differences in feel. You are comparing two different groupsets. The specs have changed for better or worse — hopefully better, of course. Additionally, I assume the 6800 is older and more worn in with more logged mileage which in and of itself could account for the difference in feel. But if you are not happy with the performance of the 8000 recheck and readjust everything again. And don’t forget the B screw adjustment for the distance between the cassette cogs and pulley wheels.
Good luck!