Just think how much changes in 20 years in car design aesthetics, never mind cutting edge stuff like computing and aircraft design. We also should factor in the alien influences on the Federation, since those new engines are supposed to be the product of research carried out on another planet entirely. There may be a lot of humans working for the Feds, but not exclusively so. I think sticking on the old engines, the thing that would almost certainly be prime candidate for replacement and upgrading in a refit, is just not right.