One interesting storyline could be a crossover where Agents of Shield agents have to team up with the Avengers to stop a powerful alien threat that neither group could handle alone. This would involve a lot of character interactions, like Coulson trying to give orders to Iron Man or Natasha Romanoff teaching some of the Shield agents her spy skills.
Definitely Coulson. He has such a rich backstory and his relationship with both the Agents of Shield and the Avengers (in an indirect way) is very interesting. His resurrection in Agents of Shield also provides a lot of potential for fanfiction. You could explore how he copes with being brought back to life and his new purpose.
A great fanfic idea could be about an old enemy from the Agents of Shield's past coming back and the Avengers being brought in to help. It could involve a lot of mystery, action, and the building of new relationships between the two groups.
One idea could be a story where the Agents of Shield team has to team up with some of the less - known Avengers to stop a new, powerful threat that is specifically targeting the more minor superheroes. This would give a chance to explore the dynamics between the two groups and shine a spotlight on the underrated characters.
Well, Tony Stark would probably be quite cocky around the Agents of Shield at first. He might make sarcastic remarks about their technology compared to his. But then he'd realize they have some unique skills and knowledge. Steve Rogers, on the other hand, would be more respectful and interested in their mission. He'd see them as comrades in the fight against evil. Natasha Romanoff might find some kindred spirits among the female agents of Shield like May. They could share their combat experiences and spy techniques.
Loki could be a great focus in a fanfiction involving both. He has a history with the Avengers, but his wily and unpredictable nature could lead to some interesting interactions with the Agents of Shield. He could be playing his own game, pretending to help both groups while actually having his own agenda. It would be fun to write about how the Agents and the Avengers try to figure out his true motives and keep him in check.
One idea could be a crossover mission where the Agents of Shield team has to work with the Avengers to stop a powerful alien threat that is targeting both Earth and a hidden Inhuman settlement. The Agents could bring their espionage skills while the Avengers use their raw power.
Perhaps there could be a time - travel related plot. A device is accidentally activated in a S.H.I.E.L.D. lab that sends some Agents and Avengers back in time. They end up in a crucial moment in history, like during World War II. There, they meet younger versions of some of the Avengers. They have to work together without changing the timeline too much while also finding a way back to their own time.
One interesting storyline could be Skye's struggle to communicate while being mute within the context of the team's missions. For example, she might develop a unique form of sign language that only the team members gradually learn to understand, which could add a new layer of teamwork and bonding. Another could be how she uses her hacking skills in a different way since she can't verbally interact as easily, perhaps finding ways to leave digital messages that are only decipherable by certain members of the team.
One idea could be that the Agents of Shield discover a new threat that is related to an old enemy of the Avengers. They have to team up to figure out how to stop it. For example, a hidden Hydra cell has found a way to re - activate an old weapon that was once used against the Avengers.