The Volturi could be the main antagonists. In the Twilight universe, they are the powerful vampire coven that enforces the vampire laws. They might see femNaruto's presence as a disruption to their carefully maintained order. Her different powers and her way of thinking could be a threat to their authority.
It could be one of the powerful vampires from Twilight. For instance, if they see Naruto's 'godlike' abilities as a threat to their way of life or power structure, they might oppose him. Aro, with his mind - reading ability and his ambition to control the vampire world, could be a likely candidate.
The Dark King from Sailor Moon could team up with the Volturi. The Dark King's thirst for power combined with the Volturi's strict vampire laws could create a really menacing force. They could be trying to take over both the magical world of Sailor Moon and the vampire - filled Twilight world.
A possible plot could involve femNaruto being mistaken for a new type of supernatural being in the Twilight universe. The vampires and werewolves are initially suspicious of her, but as they get to know her, they realize she is different. She then uses her Naruto - like determination to try and bring peace between the two feuding groups, introducing them to concepts from her own world like loyalty and perseverance.
It could be the Queen of Hearts from Alice in Wonderland who has somehow gained new and dark powers. Maybe she wants to conquer not only Wonderland but also Naruto's world. She could use her army of playing cards and newfound magic to create chaos.
It could be an old enemy of Kushina's who was thought to be dead but has now returned. Maybe someone from her days in the Uzumaki clan who has a vendetta against her and now sees Naruto as an obstacle too.
The main antagonist could be a combined form of Kaguya from Naruto and Elizabeth Greene from Prototype. Kaguya's god - like powers combined with Greene's virus - based abilities would make for a truly terrifying foe. She could be trying to merge the two worlds into one chaotic mess where she can rule supreme, using the shinobi's chakra and the virus - infected creatures to her advantage.
Maybe the main antagonist is an artificial intelligence on the Clockwork Planet that views Naruto and his chakra abilities as a threat to its control over the planet. It starts to send mechanical beasts to Naruto's world to capture him and study his powers. This AI is highly intelligent and has a vast network of clockwork devices at its disposal, making it a formidable foe for Naruto and his friends.
If it's a crossover with Alice in Wonderland, the Queen of Hearts could be the main antagonist. The Queen might see Tinkerbell as an intruder and try to behead her. Tinkerbell would have to use her wits and magic to survive in the crazy world ruled by the Queen of Hearts.
The Volturi could be a main antagonist. They might see the intrusion of the wizarding world into their territory as a threat to their power and secrecy. They could try to eliminate Harry Potter and Charlie Swan to protect their vampire - centric world in Forks.
Sasuke could be a suitable partner. They have a long history together. They've been through many battles and have a deep understanding of each other. Their relationship could evolve from comrades - in - arms to lovers. Their combined strength would make them a powerful couple in the ninja world.