One idea could be to cross RWBY characters with characters from another popular anime, like Naruto. Imagine Ruby with the ability to use Naruto's shadow clone jutsu. Another could be a crossover with the Harry Potter universe, where the RWBY characters attend Hogwarts and have to deal with magic and dark wizards. Or perhaps a crossover with the DC universe, with RWBY characters teaming up with the Justice League to save Remnant from a greater threat.
For an 'rwby prototype crossover fanfiction', you could do a crossover with the Star Wars universe. The RWBY characters could be Jedi or Sith, with their weapons and semblances adapted to fit the Star Wars setting. For example, Weiss could be a Jedi with her ice powers used in a more lightsaber - like way. Also, a crossover with the Pokémon world would be cool. RWBY characters could catch and train Pokémon to help them in their battles on Remnant.
Maybe a story where the Grimm from RWBY are infected by the virus from Prototype. This would make them even more dangerous and unpredictable. The RWBY characters would then have to figure out a way to stop the spread of this new, enhanced threat, and they might have to team up with some Prototype characters who understand the virus better.
One idea could be exploring the backstories of the characters in more depth. For example, how Ruby got started on her journey before the main events of RWBY. Another could be creating alternate universes where the characters have different abilities or roles.
One interesting idea could be a crossover of different timelines within RWBY. For example, characters from the past meet the current ones and have to deal with the differences in their worlds. Another could be a crossover of different teams in unexpected ways, like Team RWBY having to team up with a rival team to face a common enemy that is more powerful than any they've faced before. And sometimes, there are crossovers that involve alternate versions of the characters, where their personalities or abilities are slightly different, which can lead to very unique and engaging storylines.
One idea could be that the main characters from both games, Cole from Infamous and Alex from Prototype, team up to fight a common enemy that threatens both their worlds. Maybe a powerful virus that is mutating people in the Infamous universe and also causing chaos in the Prototype world.
One idea could be to explore an alternate origin for the characters. For example, what if Ruby's silver eyes were a result of a prototype experiment gone wrong? Another could be to set the fanfic in a parallel universe where the Grimm are actually created by a mad scientist using prototype technology. And perhaps a story where the characters have to use prototype weapons that have unpredictable powers.
In a Prototype - Mass Effect crossover fanfiction, a possible scenario is that the Reapers from Mass Effect encounter Mercer. Since Mercer can consume and assimilate other beings, it would be interesting to see how he'd fare against the Reapers. He might be able to absorb some of their technology or even gain new powers from them. And the way the different races in Mass Effect, like the Turians or Asari, would react to his presence would also be a great plot point.
Another concept could be that a character from Lord of the Rings, like Legolas, somehow gets transported to the world of Prototype. There, he would have to adapt to the modern - day setting and deal with the infected. He could use his archery skills and elven agility in a completely different environment. His presence might also cause a stir among the military and scientific communities in the Prototype world, as they try to figure out who he is and where he came from.
A great concept could be a story where the Prototype technology is somehow introduced into the Mass Effect universe. For example, some Cerberus scientists could get their hands on Prototype samples and start experimenting. This could lead to the creation of new, dangerous hybrids that the main characters have to deal with. Or perhaps Shepard has to team up with a character similar to Mercer to fight a common enemy that is exploiting both Prototype and Mass Effect technologies.
One interesting idea could be the unique character interactions. For example, how the RWBY characters might interact with the denizens of 'heaven' in this fanfiction. Maybe they learn new skills or gain different perspectives on their own world.
One idea could be that Superman arrives in the RWBY world and has to learn about Dust and its powers. He could team up with Team RWBY to fight a common enemy, like a powerful Grimm that is immune to normal attacks but not to Superman's strength. Another idea is that Ruby discovers she has some Kryptonian-like abilities and Superman helps her understand and control them.