Charizard and Superman. Charizard's powerful fire - breathing and flying abilities are similar to Superman's powers to some extent. They could have an epic showdown at first, thinking they are rivals, but then realize they are on the same side. Superman could learn from Charizard's more primal and instinctive fighting style, and Charizard could be in awe of Superman's more controlled and moral - based actions.
Definitely Pikachu and Batman. Pikachu's cute yet powerful appearance would contrast with Batman's dark and brooding nature. Batman could use his detective skills to figure out the mysteries in the Pokemon world, while Pikachu's electric attacks would be useful in combat. Also, the dynamic between them would be really interesting, like Pikachu trying to cheer up Batman or Batman trying to train Pikachu in a more strategic way.
Jigglypuff and The Flash. Jigglypuff is known for its singing that can put others to sleep. The Flash could use this to his advantage in battles. He could quickly carry Jigglypuff to strategic locations where it can sing and incapacitate enemies. And Jigglypuff could be amazed by The Flash's super - speed, always trying to keep up with him and getting into comical situations.
One possible plot could be that the Pokemon and Justice League members have to team up to stop an evil force that is trying to take over both the Pokemon world and the cities protected by the Justice League. Maybe a powerful, shadowy villain has discovered a way to use Pokemon powers in the human world in a very destructive way, and only by combining the unique abilities of the Pokemon and the superpowers of the Justice League can they hope to defeat this new threat.
Batman, of course, is essential as he is the Dark Knight. His brooding and strategic nature adds a lot of depth. Superman also makes a great contrast to Batman. Their different ideologies on how to use power can create interesting conflicts and collaborations. Wonder Woman is another great addition. Her warrior spirit and unique powers can bring a different dynamic, especially when she teams up with Batman for a mission.
Ash Ketchum is always a popular choice. His experience and determination can make for great storylines in the Kalos League. Serena could also be included, especially if you want to explore a romantic sub - plot or her growth as a Pokémon trainer.
Flash is always an interesting character. His super - speed gives him a unique perspective and allows for some really cool action scenes. You can explore how he perceives time differently during battles.
Well, Batman is a must - have. He is the character that can tie all the others together. Then there's Superman, who represents the ultimate power in the League. Green Lantern is also important as he brings the power of the Lantern Corps and his unique willpower. Aquaman is vital as he can connect the League to the underwater world and has his own set of powers. And of course, Martian Manhunter with his shape - shifting and telepathic abilities can add a whole new dimension to the story.
Miss Martian from Young Justice could be a great focus. Her powers of telepathy and shape - shifting make her a formidable opponent. Also, her experiences as a young hero trying to fit in and be accepted, especially when facing the more established Justice League, can lead to some really interesting character development and plot twists.
The Doctor from Doctor Who. He could bring his time - traveling TARDIS into the Justice League's universe. His wits and knowledge of different times and places could be a huge asset in solving a mystery that the Justice League is facing, and his alien nature would add an interesting element.
A third interesting storyline might involve a secret alliance between a member of the Justice League and a villain that the Young Justice team discovers. This discovery then sets off a chain of events where the Young Justice team has to decide whether to trust the rest of the Justice League and how to handle this new information without causing a complete breakdown in the superhero community.
Batman, without a doubt. He has such a rich backstory with his parents' death, his training around the world, and his determination to fight crime in Gotham. Writers can explore his complex personality, his moral code, and how he interacts with other, more super - powered members of the Justice League.
Superman might feel a sense of guilt if he could have saved Naruto but didn't. He's always about saving lives, and Naruto's death would be a blow to his self - image. Batman would see it as a mystery to solve, trying to figure out how Naruto got to their world and what led to his death. Wonder Woman would be saddened by the loss of a potential ally. The Flash might be more cautious in future battles, seeing how quickly Naruto was taken down. Green Lantern could question his own power, as Naruto had unique abilities that he couldn't protect from.