Another likely crossover could be between Giorno Giovanna and Wolverine. Giorno's ability to create life with Gold Experience and Wolverine's healing factor and berserker rage are both very unique powers. They could have an interesting relationship, either as allies learning from each other's powers or as opponents in a battle of wills.
Edward from Twilight could be a likely candidate. His brooding nature and special abilities might make for an interesting interaction with the Jedi or Sith in Star Wars. He could either be seen as a potential threat or an ally. Another would be Ahsoka Tano from Star Wars. Her strong will and combat skills could be interesting when pitted against the vampires of Twilight.
Ciri and Daenerys Targaryen. Ciri has magical powers and is a strong female character. Daenerys has her dragons and is a powerful leader. They could meet and form an alliance. Ciri might be interested in Daenerys' dragons and Daenerys could be intrigued by Ciri's magic. Together they could change the power dynamics in a fanfiction world.
Hermione and Sandy could be great for a crossover. Hermione's intelligence and love for knowledge could be paired with Sandy's scientific know - how. They could collaborate on some sort of underwater - land hybrid project, perhaps creating a new kind of magical - scientific device that works both in Hogwarts and in Bikini Bottom.
In Pokemon, Ash would be a likely candidate. He's the main character and is always up for new adventures. In Yu - Gi - Oh GX, Jaden is the obvious choice. He's brave and loves to duel. Imagine Ash and Jaden meeting. Ash could show Jaden how to catch Pokemon, and Jaden could introduce Ash to Duel Monsters. Another possibility is Misty from Pokemon. She could be interested in the magical aspects of Yu - Gi - Oh GX. And from Yu - Gi - Oh GX, Alexis could cross over. She might be intrigued by the cute Pokemon and how they are trained.
Definitely Naruto and Spider - Man. Naruto's energetic and determined nature combined with Spider - Man's quippy and heroic attitude makes for a great crossover. They could swap powers or team up to fight villains in both universes.
Loki and Draco Malfoy would be a likely crossover. Loki is the mischievous god in the MCU, and Draco is a bit of a troublemaker in the Harry Potter world. They could team up and cause all sorts of chaos. Maybe Loki would teach Draco some of his more devious tricks, and Draco could introduce Loki to the pure - blood ideology of the wizarding world, which could lead to some really interesting storylines.
Kakashi is also a favorite in these crossovers. His intelligence and wide range of jutsu, especially the Sharingan, make him interesting. In Marvel, he could be like a mentor figure to some of the younger heroes, similar to how he was in Naruto. In DC, he could be an ally to the Justice League, using his skills to outwit villains. Sakura, with her medical and combat skills, can also be a great addition, perhaps working with the Avengers' medical team in Marvel or with Wonder Woman in DC.
It's hard to say for sure, but Thanos with the Infinity Stones could be extremely powerful. However, if we consider the JoJo universe, DIO with his time - stop ability and vampiric powers is also a force to be reckoned with. If they were to face off, it would be a battle of epic proportions.
In 'jojo x marvel universe fanfiction', the idea of a Joestar character having a crossover with the X - Men is really cool. Maybe a Joestar with a stand that has mutant - like abilities could join the X - Men. It would be fascinating to see how the Joestar family's values and the X - Men's fight for mutant rights would interact.
I think a pairing between Pearl and Giorno would be really interesting. Pearl's grace and combat skills, along with her loyalty, could pair well with Giorno's determination and his ability to create life with Gold Experience. They could have some really cool fight scenes together against common enemies.