I was thinking about this the other day.
Someone had mentioned that stupid Shamalan movie "Signs" where the aliens were defeated by water, which isn't much different from "The day the earth stood still" where they couldn't breath our air.
The only legitimate reason for vaccinations is to vaccinate against FOREIGN bodies.
With worldwide travel there really isn't a huge threat of humanity coming into contact with something new.
So what does that leave?
CDC (center for disease creation) creates foreign bodies all the time, so do their foreign counterparts. A legitimate use of vaccines would be to help safeguard the public against chemical warfare.
But thinking about those SciFi movies, what if there were an alien species that would like to have contact with us, but each population had to be throughly vaccinated first to each-others diseases? It would take years, maybe generations…