I assume that all the different systems (Edge of the Empire, Age of Rebellion and Force and Destiny) will be able to work with one another. Kind of like the Warhammer 40k systems (Dark Heresy, Only War, Deathwatch, Rogue Trader, etc). But has anyone heard definitively if that's a proper assumption?
Right now, your guess is just as good and valid as anyones as to how well the three different books will work with one another. From the horror stories I've heard about Deathwatch, I'm hoping Force & Destiny does a better job of integrating with EotE & Age of Rebellion.
Given the time and effort put into developing EotE's dice system, it probably is a safe bet the fundamental mechanics regarding the dice pools will be the same across all three games. But as mouthymerc said, the tricky question is how much more powerful are PCs made using Age of Rebellion or Force & Destiny gonig to be compared to EotE PCs?