Season 2 of Agents of Shield masterfully lifted the show from its rocky begennings in season one. Season two introduced us to inhumans and many new characters as well as setting season 3 up for the secret warriors. I have made a list of potential villains, teams, characters and stories for season 3.
Captain America Civil War will hit theaters in April 2016, close to the end of season 3, and will most definantely have a huge impact on [Agents of S.H.I.E.L.D.](tag:722469). By the time the movie is made, Shield will most likely be up and running, just in time to be ripped apart by Civil War. Civil War will have a huge impact on the show due to the introduction of inhumans being introduced on the show. Civil War is a dispute between heroes about what to do with super powered beings, resulting in a massive war. There is also a rumor that Coulson and his team will assist Captain America in the movie. With Samuel L. Jackson being absent from Captain America: Civil War, it would be a marvelous oppurtunity for him to appear on the show. I believe the core of Coulson and his team will support super powered beings, such as Skye, the secret warriors and Fitz. However, it is very possible that Bobbi, Mack, and even Simmons will be against Coulson.
Defeating Rogue Inhumans
The season 2 finally resulted in many rogue inhumans appearing and will most likely be similar to the format of the Flash where each episode the team must defeat a different Villain.
Not as likely due to the Hydra Overkill form season 2, but with Ward becoming more deadly, it is possible.
Secret Warriors Characters
He will most likely fill in for Nick Fury's role in the comics as team leader and mentor of Skye
Quake, Skye, Daisy Johnson
Perhaps having the biggest season 2 transformation, Skye is now a earth shaking inhuman known as Quake. She will definantely be a team leader and be extremely influential.
Luke Mitchel will be a season regular next season and will most likely be a member of the Secret Warriors.
This is where it gets debatable. Many are curious as to whether the new team is just for natrually powered beings, or just heroes in general. Deathlok would be an awesome addition to the show.
Mockingbird, Bobbi Morse
Once again, it is debatable, but I hope she becomes a member of the team.
A valuable member of the team in the comics with super speed powers and would be a great addition.
A character with mystical powers and would eventually lead to a great Dr.strange crossover.
The son of absorbing man and a member of the team, Jerry Sledge would make a great and interesting member of the team.
Taskmaster is an amazing villain and there are many rumors with piles of evidence that suggest Ward is taskmaster. It would be amazing if he did turn into this iconic villain.
After Simmons was absorbed by the mysterious Kree object in the season finale everybody has been wondering what happened to Simmons. Gordon said the object could mean the end of inhumans. My guess is that it turned her into an inhuman with the powers of sucking the Inhuman DNA away from powered people, similar to leech in the X-men. It is possible she will remain gold, but it is more likely she will be a villain
They are a group of Asgardian criminals wrecking havoc on earth and would make a great villainous team for season 2.
This cliffhanger was never solved after The incredible Hulk in 2008 and there are many rumors that he might be a villain for season 3.