They are a pain because they can be. I know all too well from my own job what bosses are like- they come in trying to say how to do something when those that have done the job for years know perfectly well the boss' idea will not work. So, you have to try to explain to them (small words help) why their idea is not as good as how things are done now.
Fortunately most of the supervisors I have had were fellow co-workers who did not fall into the "Us vs Them" mentality you have run into. The main problem comes from the supposed manager and the higher ups from head office who haven't seen how it's done.