I tend to see humans as just another animal species, subject to pressures similar to those of other mammals. Whenever disease comes up it seems like vaccinations are the only factor discussed.

Can anyone here speak to other factors (at a macro scale) that influence human health over large spans of time?

The main factor (at a macro scale) that influences human health over large spans of time is, in fact, large spans of time.

Specifically, no human has yet, or ever will, live long enough to qualify as a large span of time.