I'm not really a baseball fan any more, but I think that you can only compare greatness across generations, by referring to one's greatness relative to one's generational peers.
The thing is, great athletes (and others, I guess) rise to meet their competition. When the competition increases in intensity (i.e. pitchers start throwing faster, yadda yadda yadda) then the batters must compensate by improving themselves. Sure Ruth never faced any great pitchers by modern standards, but maybe if he had, he would have lost some weight and gained some control and been just as good (relative to other players) now as he was then. He didn't have to do so back then, though, so he didn't. He could dominate the game while remaining a fatass.
Time results in better technologies, drugs, techniques, etc. that improve every aspect of a sport. Hell even something as simple as a new shoe technology could make a difference. But as long as it imparts that difference equally among all teams/players, there's really no difference made. Sure they can hit longer balls or run faster or whatever, but they can do so only in the face of stiffer competition from other teams and players.