One great 'Merlin Crossover with Avengers' fanfiction is 'When Merlin Meets the Avengers'. It has an interesting plot where Merlin's magic gets him noticed by SHIELD. Another good one is 'Merlin in the Marvel Universe'. It shows how Merlin's wisdom and magic skills can be used to solve some of the Avengers' toughest problems.
One idea could be that Merlin uses his magic to help the Avengers in a battle against a powerful magical enemy. Maybe he disguises himself as a normal human at first and then reveals his true powers when the situation is dire.
The Avengers would also have to adjust to the social and cultural norms of Camelot. They can't just barge in and start making demands. Merlin would have to act as a mediator between the two groups. He would explain to the people of Camelot that the Avengers are there to help, and at the same time, he would make sure the Avengers understand the importance of respecting Camelot's traditions. This interaction would create a lot of interesting storylines and character development opportunities.
One popular trope is the 'fish - out - of - water' story. Merlin, coming from a medieval world, is suddenly in the modern world of the Avengers. It's funny to see his reactions to things like technology. Another is the 'power - sharing' trope. Merlin's magic and the Avengers' powers combine in unique ways to defeat enemies.
Merlin could bring his magic to the Avengers. His knowledge of ancient spells and potions might help in battles against powerful foes. For example, he could use magic to disarm enemies or create protective shields.
Maybe in the fanfic, Batman's rogues gallery somehow teams up with some of the Avengers' villains. This forces Batman and the Avengers to work together. Batman could introduce his unique gadgets and combat style to the Avengers, while they could show him their superpowers up close. For example, Iron Man could be intrigued by Batman's utility belt and try to create his own version of some of the gadgets.
A good plot could involve a villain from the Homestuck universe creating chaos in the Avengers' world. The Homestuck characters come to help, but there are misunderstandings at first between them and the Avengers. However, as they start to understand each other's powers and motives, they form a strong alliance to defeat the villain.
Teamwork is also a major theme. Since the characters from both universes have different skills and knowledge, they have to learn to work together. In many fanfics, we see Merlin teaching the Winchesters about his kind of magic, and in return, the Winchesters showing Merlin how to deal with the more modern - day and dangerous supernatural entities. This theme of cooperation is what makes the crossovers so interesting.
One great 'Merlin and Harry Potter' crossover fanfic is 'The Merlin Effect in Hogwarts'. It combines the magic systems of both universes really well. The characters from Merlin, like Merlin himself, fit surprisingly well into the Hogwarts setting. They interact with Harry and his friends in interesting ways, for example, Merlin uses his unique magic to solve some of the problems at Hogwarts that the students there are facing. It's a fun read for fans of both series.