One creative plot twist could be that Viewtiful Joe's VFX powers start to malfunction in the School DxD world. This could lead to all kinds of chaos as he tries to control his powers while dealing with the devils and other supernatural beings in School DxD. Another could be that the characters from School DxD gain some of Joe's powers temporarily and have to learn how to use them in their own battles, which would completely change their fighting styles.
Joe would probably be very confused at first in the School DxD world. He's used to his own kind of battles, and suddenly being in a world full of devils, angels, and other mythical creatures would be a shock. He might be very cautious and try to figure out who the good guys and bad guys are. The devils in School DxD might be intrigued by Joe's powers and either try to recruit him or study him. The angels, on the other hand, might be more suspicious and see him as a potential threat at first.
How about a crossover with Sonic the Hedgehog? Picture this: Sonic is running through a strange new zone and accidentally enters Joe's world. They join forces to stop Dr. Eggman who has somehow teamed up with one of Joe's enemies. Sonic's speed and Joe's Viewtiful powers would create a really fast - paced and exciting story.
A great plot could involve a powerful enemy that has the ability to drain the 'viewtiful' energy from Joe. Tsukune and his friends notice the weakened Joe and decide to help. They all train together, combining their different powers and skills. The story could then build up to an epic showdown where they all have to use their combined strength to defeat the enemy and Joe regains his full 'viewtiful' power.
Maybe a character from Halo, like Master Chief, gets transported into the GI Joe universe. He has to adapt to their different warfare style and politics. Meanwhile, the GI Joe characters are in awe of his advanced armor and combat abilities. This creates a lot of interesting interactions as they try to figure out how to send him back while also using his skills to fight their own enemies.
Well, perhaps a plot twist could be the mixing of the two worlds' forms of magic. Naruto's world has its own kind of jutsu - based magic, while High School DxD has demonic and angelic magic. If these magics were to merge in some characters, it would create really unique abilities. For instance, a character could use a jutsu while also having the ability to summon angels or devils. Another interesting plot twist could be that the Nine - Tails (from Naruto) somehow gets involved in the Rating Games in High School DxD. It would be a huge advantage or a major disruption depending on how it's handled. And what if a character from High School DxD learned the Shadow Clone Jutsu? They could use it for all sorts of mischief or strategic advantages in their own world.
One possible plot twist is that the hogyoku from Bleach somehow ends up in the hands of a character in Highschool DxD. This could lead to a character attempting to use it for their own gain, perhaps to gain ultimate power over both the devils and the angels. Another interesting plot twist is that a character from Highschool DxD gets reincarnated as a Soul Reaper in Bleach. They would have to learn the ways of the Soul Reapers while still retaining some of their previous abilities and memories. This could create some really interesting character development. A third plot twist could be that the balance between the three factions in Highschool DxD (devils, angels, and fallen angels) is disrupted by the arrival of Hollows from Bleach. The factions would have to figure out how to deal with this new threat, and it could lead to some unexpected alliances.
The interaction between Viewtiful Joe and Moka would be really interesting. Moka's vampire powers and Joe's 'viewtiful' abilities could create some really cool fight scenes. Also, their different personalities - Moka's shy - vampiric duality and Joe's confident heroism - would make for some great dialogue and character development moments.
Inklings from Splatoon could also be fun to include. The Inklings' ink - based attacks and their unique culture could add a new dimension to the story. They could team up with Joe to stop an enemy that is trying to cover both their worlds in some sort of dark, gooey substance. Joe would have to figure out how to work with the Inklings' different combat style.
One of the most creative plot twists could be when Naruto gains the ability to use the Predator's cloaking technology in a fight. It would completely catch his opponents off - guard. Another could be if an Alien queen somehow forms an alliance with Orochimaru, combining their unique and deadly abilities. And also, a plot twist where the Predators see Naruto as a worthy opponent not just for his strength but for his indomitable spirit, which goes against their usual view of prey.
Perhaps a plot twist where the pilots from Infinite Stratos are suddenly transported to the Gundam universe and have to adapt. They might find that the rules of combat are different, and the political situations in the Gundam universe are far more complex. Their presence could also stir up new rivalries or alliances between different factions in the Gundam world. This would not only be a shock for the IS pilots but also for the Gundam characters who have to deal with these new arrivals.