Well, one way the storylines could blend is through the character interactions. In Tokyo Ghoul, the ghouls have a complex society and set of rules. In Rosario Vampire, there are various supernatural beings. If the two universes crossed over, perhaps the ghouls' need for human flesh could be in conflict with the vampires' need for blood in Rosario Vampire. Maybe some characters from each side would form alliances to deal with this new, complex situation.
A new character could be a hybrid of a ghoul and a vampire. This character might have the strength and speed of both species. They could struggle with their dual nature, being attracted to both human blood and flesh but also having a sense of morality from both the ghoul and vampire worlds.
In a Rosario Vampire Tsukune Ghoul fanfiction, Tsukune might face new challenges. He could be hunted by anti - ghoul organizations because they mistake him for a ghoul due to some new power he has acquired. This would force him to prove his innocence and also learn more about the world of ghouls in the process.
One possible plot could be a character from Tokyo Ghoul ending up in the world of Vampire Knight. Maybe Kaneki, with his unique ghoul powers, could interact with the vampires and hunters in Vampire Knight. He might initially be seen as a threat, but as the story progresses, they could find common ground in their struggle for survival in a world that fears them.
I'm not sure if there is such a specific fanfiction where a character from Rosario Vampire is reading Naruto fanfiction. Fanfiction can be very diverse, but this seems like a rather unique and specific concept. It's possible that it might exist in the vast realm of fan - created stories, but it would be quite difficult to find without a more targeted search.
Rosario Vampire and Tokyo Ghoul are both very popular in the anime and manga world. A fanfiction combining Tsukune from Rosario Vampire with elements of ghouls could be really interesting. It might explore how Tsukune, who is already in a world full of vampires, werewolves and other supernatural beings, would interact with ghouls. Maybe he would form an alliance with some ghouls against a common enemy in the Rosario Vampire world.
A possible plot could be that a powerful artifact in the Rosario Vampire world is being targeted by both Hollows and some rogue vampires. Ichigo and Tsukune find themselves on a quest to protect it. Along the way, they encounter various challenges and meet different characters from both universes. The cultural shock between Ichigo's world of Soul Reapers and Tsukune's world of monsters and humans could also add some comedic and interesting elements to the story.
Kaneki and Zero could make an interesting pairing. Kaneki has his inner turmoil with his ghoul side, and Zero has his own battle against his vampire nature. They could bond over their struggles to control their 'dark' sides and their determination to protect the ones they care about.
Power struggle is a common theme. You have the super - powered beings from Prototype and the ghouls from Tokyo Ghoul, all vying for control or survival in a merged world.