Perhaps when they combine, Spider - Man gets the ability to fly due to Captain Universe's power. He could also have a sort of cosmic - awareness, being able to sense threats from across the universe. This would make him an even more formidable hero, able to protect not just his city but also have a role in the greater cosmic balance.
Their powers could combine in a way that Naruto's chakra enhances Spider - Man 2099's physical abilities. For example, his strength and speed could be increased even more. Also, Spider - Man 2099 could use Naruto's shadow clone technique to create multiple copies of himself to confuse enemies while swinging around on his webs.
Another way their powers could combine is in the area of mobility. Spider - Man can move quickly through the city, but Elsa can create ice bridges and paths that can cross large gaps or even over water. So, if they were on a mission together, they could use these combined abilities to get to places faster. For example, if they were chasing a villain who escaped to an island, Elsa could freeze a path across the water and Spider - Man could swing them both along the path at high speed.
Obviously, Spider - Man is one of the main characters. He's the one who gets the Captain Universe powers. And Mary Jane Watson might also be a main character as she's an important part of Spider - Man's life. Another could be J. Jonah Jameson, who always has an interesting take on Spider - Man's activities, especially when he becomes this more powerful version.
Loki's illusions combined with Spider - Man's acrobatic skills would be a great combination. Spider - Man could move within Loki's illusions, confusing their enemies even more. And if Loki were to use his telekinesis to move objects, Spider - Man could use his webs to direct those objects towards their enemies. Also, Spider - Man's ability to stick to walls could be used in Loki's lairs or magical structures, allowing him to navigate them more easily while Loki uses his magic to deal with any traps or guards.
Well, Spider Man's ability to sense danger and his super - agility would be great for getting into and out of tight spots. Valkyrie's strength and her enchanted sword could be used for direct combat. In a story, they could combine their powers like when facing a horde of enemies. Spider Man could web up some of the foes, and Valkyrie could then easily dispatch them with her sword. Also, Spider Man could use his webs to create distractions while Valkyrie sneaks up on the main villain.
One interesting aspect could be the unique powers Spider - Man gains as Captain Universe. It makes for really cool action scenes. For example, his strength and agility could be enhanced to an even greater degree than his normal powers. Another aspect is how his character might change in the fanfic. Maybe he becomes more self - assured or takes on more global - scale threats.
Spider - Man's powers of super strength, agility and web - slinging could combine with Kung Fu Panda's martial arts skills in a really interesting way. For example, Spider - Man could use his webs to create complex traps while Kung Fu Panda uses his kung fu to lure enemies into them. Also, Spider - Man's ability to sense danger could be enhanced by Kung Fu Panda's understanding of chi flow. If an enemy is about to attack from a certain direction, the combined chi and spider - sense could give them an even earlier warning.
White Tiger has great combat skills and agility. Spider - Man has his super strength, web - slinging ability, and spider - sense. In a fight, Spider - Man could use his webs to create barriers or traps for the enemies, while White Tiger could use her agility to quickly move around and attack from unexpected angles. Their combined powers would make them a very formidable team.
In a fanfiction story, their powers could combine in really interesting ways. Black Panther's ability to store and release kinetic energy through his suit could be used in conjunction with Spider - Man's acrobatic skills. Picture Spider - Man leaping into the air and Black Panther using his suit to give Spider - Man an extra boost of energy at the right moment. Also, Spider - Man's spider - sense could warn them both of incoming danger, allowing Black Panther to better strategize with his combat skills. They could also use their combined skills to create unique attacks. For instance, Black Panther could hold onto Spider - Man while he swings and then they could both attack an enemy from different angles.
Spider - Man's agility and web - slinging could be used in tandem with the Guardians' ranged attacks. For example, he could web up enemies and then Star - Lord could shoot at them while they're immobilized. Or Gamora could use Spider - Man as a distraction, swinging him around with his webs to confuse opponents, and then she could move in for a stealthy strike.