Can someone explain to me the differences/advantages on the FOX forks for the three Missions?
According to the website the Mission 1 has a Fox 34 Float while the Mission 2 and Mission Pro have the Fox 36 Float. Both are 160mm travel. The Fox 36 has larger diameter stanchions that make it more beefy/rigid and handles the really rough stuff better than the Fox 34 can. The Fox 34 is lighter and less expensive, but less capable.
I have the 2016 Mission Pro, It comes with the Fox Factory Float 36 fork with the fit cartridge. Basically it has more options for tuning how the fork responds. You have an adjustment for High and Low speed compression, and High and Low speed rebound. It also comes standard with Fox's Kashima coat on the stanchions.
A buddy of mine has the new Mission 2, still a Fox 36, but not the Factory. It offers a more simplistic adjustment on the way the fork responds, with a 3 position level, and lacks the kashima coat.