Only during the augmentation process did the s-3 have a better survival rate and thats because they didnt have what was being put into them like the s-2's did, but in combat s-2 are far superior to the s-3, the s-3 are just cheaper versions. The s-2 all had something that made them specail Kelly was abnormally fast for a 6 year old john was extremely lucky and would take on groups of other kids during playtime at school king of the hill he never lost, Kurt had this ability to sence danger he even beat john sometimes all the s-2's had something that had halsey hand pick them, the s-3 didn't have this quality the colonal just picked random orphins. in the book ghost of onyx there spi armor was suppose to fill in what they lacked so it made them somewhat invisable. S-3 and a lower suvival rate during real combat
It wasn't that the augmentation was perfected its because Kurt changed the "recipe" that was put into the s-3's