I would like to set it up so that an instructor could sit in the co-pilots seat and make weather changes happen on the fly.If sitting right seat is the answer to the instructor module then how come they left this part out?

There are many things that are disabled in shared cockpit, this is just one of them. What I do is decide on what weather I want to fly in, pull up the NOAA radar (US), find an airport with what I am looking for, select real world weather in FSX, and launch. That gives you a bit of variability.If we are doing specific training then I set the specific weather manually before starting the session. Thats the only options I know of.