Sue Storm could be a great character to focus on. In a crossover, she could use her force fields in new and creative ways. Maybe she has to protect Spider - Man from some of his more dangerous enemies when he's outnumbered. Also, her relationship with Reed Richards could be explored further in the context of a crossover. How would she react to Spider - Man's more impulsive nature? And how would she use her powers to help Spider - Man and the Fantastic Four work together more effectively? There are a lot of interesting storylines that could be developed around her.
I think Spider - Man himself would be the most interesting. He's a young and relatively inexperienced hero compared to the Avengers. His different perspective and his unique powers like climbing walls and the spider - sense would add a lot of flavor to the story. He could also bring in a sense of humor and a bit of naivete that would contrast with the more jaded Avengers.
One interesting pairing would be Reed Richards and Bruce Banner. Reed's scientific genius combined with Banner's knowledge of gamma radiation could lead to some amazing scientific breakthroughs while they're trying to solve a problem together. They could also have some great conversations about the risks and rewards of scientific experimentation.
Thor and the Thing would make a great pairing. Thor is a god with a hammer and the Thing is a big, strong rock - like guy. They could have some epic battles together against common enemies. And in between the fighting, Thor could be trying to understand the Thing's more down - to - earth view of things, while the Thing could be in awe of Thor's godly powers.
Raphael could be really interesting. In the 2003 version, he is hot - tempered and tough. In the 2012 version, he also has a strong personality. Seeing how he reacts to his counterpart and how they might either clash or bond could be a great focus. Maybe they have a friendly rivalry as they compare their fighting skills.
Ross could be really interesting. Since he's an archaeologist, in a crossover with a show like 'Indiana Jones' (in a fanfiction sense), he could go on an adventure with Indiana Jones. Ross would bring his academic knowledge while Indy would have the practical experience. Their interactions would be filled with Ross trying to over - analyze everything and Indy just wanting to get the job done.
Chiaki Nanami could be an excellent choice. She is the Ultimate Gamer, so if you cross her with a digital or virtual world, there are so many possibilities. She could use her gaming skills to navigate through a new digital realm, like a Matrix - like world. Her calm and intelligent nature would also make her a great character to lead the group in a crossover situation. She could figure out the rules of the new world quickly and help the others adapt.
One possible plot could be that Doctor Doom teams up with some of Spider - Man's villains like Green Goblin. The Fantastic Four and Spider - Man have to put aside their differences and work together. Spider - Man's agility and quick thinking combined with the Fantastic Four's unique powers would make for some great action scenes. For example, Spider - Man could swing in and save Sue Storm when she's in trouble, and in return, the Human Torch could help Spider - Man by burning away some of the webs that his enemies have trapped him in.
One of the most interesting character combinations would be between Spider - Man and the Commander from Sky High. The Commander has a lot of experience leading heroes, and he could mentor Spider - Man in some ways. Also, they could work together to train the younger heroes. And if we consider Mary Jane and Magenta, Mary Jane's charm and Magenta's magnetic powers could create some really fun and unexpected interactions. Magenta could use her powers to help Mary Jane in dangerous situations, and Mary Jane could use her wits to keep Magenta out of trouble.
The interaction between Spider - Man and Iron Man would be really interesting. Iron Man could be like a mentor to Spider - Man, providing him with new and advanced technology for his suit. Spider - Man, on the other hand, could teach Iron Man a thing or two about being a more down - to - earth hero, as he often deals with street - level crime. Their banter would be great, with Iron Man making sarcastic remarks and Spider - Man coming back with his quick - witted responses.
Definitely Naruto and Spider - Man themselves. Their personalities are so different. Naruto is loud, energetic and always eager to prove himself. Spider - Man, on the other hand, is more of a quippy and responsible hero. When they interact, there would be a lot of banter. Another interesting interaction could be between Naruto's Sensei, Kakashi, and Spider - Man's mentor, like Uncle Ben in spirit. They could exchange wisdom about guiding their young proteges.