Another option could be Mr. Sinister. He might see potential in Rogue's powers and try to manipulate her. He could also see Nightcrawler as an obstacle in his plan to use Rogue. So he creates various schemes to drive a wedge between them and make Rogue come under his control.
Another possibility is that the main antagonists could be the leaders of the other ninja villages. They might view Naruto's godlike and rogue status as a danger to the balance of power among the villages. So, they could form an alliance against Naruto, leading to a lot of political intrigue and conflict in the story.
The Leaf Village authorities could be the main antagonists. Since Naruto is now considered a rogue, they would be the ones trying to hunt him down. They might see him as a threat to the village's stability and security.
A possible plot could be set in an alternate universe where mutants are accepted in society. Nightcrawler and Rogue meet at a mutant - friendly event. Nightcrawler is performing his acrobatic feats and Rogue is instantly drawn to his charm. They start spending time together, sharing their experiences of being mutants, and slowly their friendship blossoms into a romantic relationship.
The Brotherhood of Mutants could also be antagonists. They might view the pregnancy as a sign of the X - Men becoming too domesticated and vulnerable. They could launch attacks on the X - Mansion in an attempt to disrupt Rogue and Logan's new - found family situation.
The main antagonists could be the official Avengers themselves. Since Peter Parker has joined the rogue Avengers, the main Avengers group might see them as a threat to the order they are trying to maintain. They could try to stop the rogue Avengers from achieving their goals, which would put them in direct conflict with Peter and his new allies.
It could be a group of rogue ninja who have a vendetta against Naruto. They might see his new status as a rogue as an opportunity to take him down. Maybe they were once defeated by Naruto when he was in the village, and now they want revenge. Also, there could be some hidden shinobi clans within the village who oppose Naruto's new path and try to stop him for their own reasons, like protecting the village's reputation or their own power within the village.
The Saiyans could also be antagonists. If they discover Black Goku's true nature and his alliance with Zamasu, they would likely oppose them to protect their race and the universe.
One idea could be a story where Nightcrawler and Quicksilver team up to stop a powerful villain who is causing chaos in the city. Their different powers would complement each other well. Nightcrawler could use his teleportation to surprise the enemy and Quicksilver could use his super speed to quickly disarm any traps or threats.
It could be a powerful mutant who wants to use Nightcrawler's teleportation abilities for his own evil purposes. He might see Nightcrawler as a key to achieving some sort of world - domination plan.
Ruby is often involved. Since she's the main protagonist in RWBY, it makes sense for her to interact with Nightcrawler in fanfictions. Their different powers and personalities can create interesting dynamics.