Thor is often very popular. His god - like powers and his noble personality make him a great character for fanfiction. Writers can explore his relationships with the other Avengers and his connection to Asgard.
One interesting plot could be the Avengers facing an ancient, all - powerful cosmic entity that threatens to destroy all of existence. They have to combine their powers in ways they never thought possible, like Iron Man's technology with Thor's magic.
A really cool crossover idea would be the Avengers trying to understand the Transformers' technology. Iron Man, being a tech - genius, would be fascinated by the Autobots' transformation ability and their energy sources. He might try to reverse - engineer some of it, which could lead to some interesting plot twists. And the Hulk could be an unexpected ally in battles against the Decepticons, using his brute strength to take on the powerful robots.
Well, Iron Man and Ratchet might start off on the wrong foot. Iron Man, with his cocky attitude, might try to show off his tech to Ratchet, who would be unimpressed and critical of Stark's technology in comparison to Cybertronian tech. But they could later come to respect each other's skills.
A great plot could be that a powerful artifact from the Transformers universe is found on Earth and it has the power to either save or destroy the planet. The Avengers initially think it's a new weapon or power source, while the Autobots know its true origin. They have to convince the Avengers of its importance and together protect it from the Decepticons and any other villains who want to use it for their own evil purposes.
Optimus Prime and Thor would be a really interesting pairing. They are both noble leaders. Optimus with his wisdom and strength, and Thor with his godly powers. They could exchange ideas about leadership and honor while fighting side by side against powerful foes. Their weapons are also quite interesting to compare - Optimus' ion blaster and Thor's hammer.
A plot could revolve around the Avengers Prime traveling through time to prevent a future disaster that they somehow caused. Along the way, they meet different versions of themselves and have to make tough decisions about changing the timeline.
One possible fanfiction could be about Sentinel Prime and Optimus Prime having to work together to save Cybertron from a new, powerful enemy. They might start off with some differences in their approaches but gradually learn to combine their strengths.
One possible fanfiction could be about Dark Optimus Prime's origin. Maybe he was corrupted by a powerful dark energy source in the Transformers Prime universe. This could lead to him having different goals and motives compared to the regular Optimus Prime, like ruling Cybertron with an iron fist instead of leading it to peace.