If you play with Toughness in Advanced Warfare, you'll need to choose another perk if you decide to play Black Ops 3.
Toughness isn't featured in the Black Ops 3 beta and it probably won't it arrive in the final version of the game either. The company has left the door open for a return but we wouldn't hold our breath at this point.
In response to complaints, Treyarch says that it's evaluating "high and first damage flinching for sure." So the amount of flinch could change between now and the public release in November. We'll see.