Eaton never really got any better. He was a very good defensive player but a huge liability on offense. His PER hovered around 10-12 his whole career.
Gobert on the other hand is nearly as good defensively (even if he averages a block or two less, he rebounds at a higher rate) and is light years ahead of Eaton already and he's only scratching his potential. His PER jumped from 12.9 last year to 21.9 so far this year.
I don't think there is any question (barring injury) that Gobert will be far better.