One common theme is the clash of different power systems. For instance, when Earthbound crosses with a superhero - themed story, Ness's psychic powers interact with the superpowers of the superheroes in unique ways.
Another theme is the exploration of different worlds. In an Earthbound and Zelda crossover, the characters have to adapt to the new environment of Hyrule. They might struggle with the different monsters and the way the world operates compared to Onett or Twoson.
One common theme might be growth. Jeff and Tony could be shown developing as characters within the fanfiction. For example, Jeff might become more confident in his abilities with Tony's influence. Also, loyalty could be a theme. They could be depicted as being loyal to each other no matter what difficulties they face. In addition, the theme of discovery might be present. They might discover new things about themselves or their world together, which is often an interesting aspect in fanfictions about them.
A really unique 'earthbound crossover fanfiction' is the one that crosses it with 'Undertale'. The two games have a somewhat similar aesthetic in terms of the quirkiness of their characters. In this crossover, you can see the characters from Earthbound interacting with Sans and Papyrus in the Underground. It's full of humorous moments and interesting plot twists.
Love, in a broader sense, is a common theme. It doesn't have to be romantic love but also love for their friends, family, and the world they are trying to save. Another theme is courage. They are constantly facing dangerous situations and need to be brave. In some fan fictions, Ness and Paula have to overcome their own fears to be able to move forward. And the theme of hope is also there. No matter how difficult the situation is, they always have hope that they can make things right.
A common theme is the struggle for acceptance. The minotaur, being a different and often feared creature, usually has to fight to be accepted in the new world or by the new group of characters it crosses over with.
One common theme is power struggles. Since there are different powerful characters from various planes, they often clash over control or resources. For example, in many fanfictions, two powerful planeswalkers might fight for dominance over a newly discovered plane.
Power is a common theme. Since Vegeta is extremely powerful, seeing how his power compares to characters from other universes is always interesting. Another theme is culture clash. For instance, when Vegeta enters the Harry Potter world, his Saiyan warrior culture clashes with the wizarding culture. Pride is also a theme. Vegeta's Saiyan pride often plays a role in how he interacts with characters from other fandoms.
Survival is also a big theme. Characters in the crossover fanfiction usually have to figure out how to survive in the presence of Annabelle, especially if they come from a world where they're not used to such malevolent supernatural forces.
One common theme is the idea of redemption. Raphael, who has a somewhat dark past in the original lore, often goes through a journey of redemption in these crossovers, especially with Simon's influence. Another theme is friendship. Despite their differences, they form a strong bond.
Another theme is power exploration. Naruto and Sakura have their own set of powers from the Naruto universe. When they are in a crossover, they often have to figure out how their powers work in relation to the new world they are in. This can lead to some really interesting battles and power - up moments as they learn to adapt and use their skills in new ways.
The theme of redemption also shows up sometimes. Despite being a fearsome character, in some crossovers, Deathwing might be given a chance to redeem himself. Maybe he caused a lot of destruction in his original world, but in the crossover world, he has the opportunity to do good deeds and change his reputation.