Agents of Shield hit us hard with The Inhumans and Hydra in season two, but that's over now, and a new season's on it's way! What will be the focus of season three?
The Secret Warriors will be their main focus, since at the end of season two, they hinted at it quite heavily. I am personally all for this, because I love super powered people, and a team of them fighting Ward, plus, the other Inhumans would be great.
The Skrulls: I would love to see the Skrulls start to be introduced slowly into season three. They would be a threat that no one would expect. The way they could be introduced is like this: they send a scout to our world, they have a run- in with the Inhumans and Shield, but they escape, telling their leader that earth will soon be ready for an invasion. Though I doubt this will happen, as I see the Skrulls being a MCU phase four villains,but there is always hope:) More implications that Skrulls are coming, is that the Secret Warriors is being formed and, in the comics, the Secret Warriors fought the Skrulls.
Removing the last heads of Hydra will most likely be a minor focus on season three, because Hydra is nearly gone.
The Civil War will also effect the show in a major way, I hope. Since the amount of super powered people in the world is increasing, I'm sure the governments will be afraid of the Inhumans that the [Agents of S.H.I.E.L.D.](tag:722469) have been trying to keep secret from the world. I also believe the team will split, during this time, half of them agree with the government, and the other half not.
Thanks for reading:)