Definitely Coulson and Iron Man. Coulson is a big fan of Iron Man in the show, and seeing them interact would be great. Iron Man's sarcasm and Coulson's more straight - laced nature would create some really interesting banter.
Skye and Hawkeye could be an interesting pairing. Skye has her hacking and combat skills, and Hawkeye is an expert marksman. They could learn from each other. Maybe Skye could teach Hawkeye some new tech - related skills, and Hawkeye could show Skye some advanced archery techniques. Also, their different backgrounds, Skye coming from a more underground world and Hawkeye being an Avenger, would make for a cool dynamic.
I think Natasha Romanoff and Melinda May would be an interesting pair. Both are strong, badass women with a lot of combat experience. They could share their stories of their past missions, and also train together. Maybe they could even have a friendly competition to see who is better at hand - to - hand combat or espionage.
I think the interaction between Bruce Banner and Fitz - Simmons would be fascinating. Fitz - Simmons are brilliant scientists, and Banner is a scientific genius himself. They could collaborate on some new scientific research, like finding a way to control the Hulk better or developing new energy sources. Also, Clint Barton and Skye could have an interesting dynamic. Clint's no - nonsense approach and Skye's hacker - turned - agent background would make for some great banter and teamwork.
Another interesting pairing could be Batman and Daisy Johnson. Daisy has her inhuman powers, especially her seismic abilities. Batman could be intrigued by her powers and try to find ways to use them effectively in combat. And Daisy could learn a lot from Batman's combat training and his no - nonsense attitude towards fighting crime. They could form a strong duo when it comes to facing enemies that require both brute force and strategic thinking.
One really interesting character pairing could be Fitz - Simmons and the TMNT as a whole. Fitz - Simmons are brilliant scientists, and the turtles are a scientific anomaly. They could study the turtles and their mutagenic origin. The turtles could also benefit from Fitz - Simmons' knowledge of advanced technology. Another pairing that would be cool is Agent Ward (assuming he's not evil in this fanfiction) and Leonardo. Ward is a skilled agent, and Leonardo is a skilled ninja. They could exchange fighting and survival skills, and their different perspectives on loyalty and duty could lead to some interesting story arcs.
I think Daisy Johnson would be really interesting. She has her unique powers and a complex backstory from her time in SHIELD. In a crossover, she could interact with the likes of Thor. Maybe she could learn some new ways to control her powers from him, as he has experience with his own godly powers. And she could also show the Avengers her skills in combat and stealth that she learned in SHIELD. It would be fascinating to see how she holds her own among the super - powerful Avengers.
I think the interaction between Coulson and Captain America would be really interesting. Coulson is a big fan of Captain America, and Steve would be impressed by Coulson's leadership and the way he holds his team together. They could exchange stories about their different experiences in the war - Steve from World War II and Coulson from more modern conflicts.
A very interesting pairing would be Daisy Johnson (Quake) and Cyclops. Daisy has her powerful seismic abilities and her experience in the field with Agents of Shield. Cyclops has his leadership role in the X - Men and his optic blast power. They could work together on a mission where they need to combine their powers. For example, Daisy could create seismic disruptions to distract enemies while Cyclops uses his optic blast for a direct attack. Their different leadership styles could also lead to some interesting character development as they learn from each other during the mission.
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.
Definitely Naruto and Hulk. Just imagine Naruto trying to calm down the Hulk when he's angry. It would be hilarious. And on a more serious note, Naruto's positive energy might have an effect on the Hulk. Also, Sakura and Captain America. Sakura is a strong - willed and powerful female character, and Captain America is a symbol of leadership and justice. They could bond over their shared values and exchange fighting strategies.
Sam Winchester and Bruce Banner would be an amazing pairing. Sam is highly intelligent and well - read, and Bruce is a brilliant scientist. They could bond over their knowledge and maybe even find a way to control the Hulk better. Also, Natasha Romanoff and Charlie Bradbury would be a cool pair. They're both strong, independent women with a lot of skills. Natasha could teach Charlie some combat moves, and Charlie could introduce Natasha to some cool geeky stuff like LARPing.