He won the Vuelta more times.
Also, he rode in an era where there were other good riders.
Jokes aside, imagine if WW2 hadn't made the cycling calendar lie dormant for five years in the middle of Bartali's and the beginning of Coppi's careers. Their stats could have been completely insane.
Coppi was more "lucky" that he turned 20 just when the war broke out and was still only 26 when racing resumed in the spring of '46, Bartali literally lost his prime, not even Thys with WWI lost so much.
Just look at Bartali situation for the Tour by his age:
*21 - not selected, was riding in Spain.
*22 - no italian team in the race.
*23 - crashed out in yellow after winning the first alpine stage.
*24 - won obliterating the field in the hardest alpine stage.
*25 - no italian team invited to the race.
*26 - no race.
*27 - no race.
*28 - no race.
*29 - no race.
*30 - no race.
*31 - no race.
*32 - no race.
*33 - no italian team invited to the race.
*34 - won in one of the most dominant showing ever seen, he won all five mountain stages of which three alpine stages in a row gaining half an hour over his closest rival and former leader Bobet in three days and also the Ardennes stage and another one, not happy with that he dropped everyone even on the cobbles en route to Roubaix in the second last stage, before puncturing and being catched by the first chase group, and attacked again also in the last stage.
*35 - 2nd after being forced to wait and work for Coppi and then being abandoned by the team car after a puncture while in yellow.
*36 - abandoned after the Aspin accident.
*37 - 4th.
*38 - 4th after working for Coppi.
*39 - 11th.
*40 - not starting.