The #1 difference would probably be the extent of the Black Death. I read this book on the Black Death back in high school in the 90s and the ideas they came up with to try to stop it were both ingenious and sad. Some concluded that it was due to not enough filth (too much cleanliness results in a body unsuited to the natural environment) and would put their faces into latrines and whatnot to try to breathe in as much of that fetid air as they could, some tried to use gold alloys, and so on. Just a little bit of knowledge on how disease worked would have done wonders.
That reminds me, there was also that Star Trek TNG episode where Data unknowingly brought radioactive metals into a village that was similar to that. They also had a kind of science of their own based on five elements that functioned at times but was also extremely inaccurate elsewhere, and Data invented a microscope while staying with them.