Perhaps a rogue Sekirei who has been corrupted by the power of the Juubi's energy that has seeped into the Sekirei world. This Sekirei could start causing chaos, believing that they are now more powerful than the others and should rule over them. Naruto would then have to stop this Sekirei from causing more destruction and bring balance back to the Sekirei world.
Another option could be a group of ninja from the Naruto world who are jealous of Naruto's power, including the Juubi's power, and they team up with some anti - Sekirei forces in the Sekirei world. Their combined goal could be to steal Naruto's power and use it to take over both worlds. They would be a formidable antagonist as they have knowledge of ninja techniques and the Sekirei Plan.
Madara Uchiha could be a great antagonist in this fanfic. Even though he was defeated in the original Naruto story, if he somehow gets resurrected and gets a chance to control the Juubi, he would be a formidable foe. He already had grand plans for the world in the original story, and with the Juubi's power, he could be even more dangerous. He might want to reshape the world according to his vision, and Naruto would have to fight him once again to protect everyone.
One possible plot could be that Naruto somehow gets involved in the Sekirei Plan while still having the power of the Juubi within him. He might use his ninja skills and the Juubi's power to protect the Sekirei from those who would use them for evil purposes. For example, he could face off against Minaka Hiroto, the creator of the Sekirei Plan, if he discovers that the plan is causing harm to the Sekirei. Naruto's values of friendship and protecting the weak would likely drive his actions in this fanfic scenario.
It could be an evil version of the Sage of Six Paths. He might want to take the Juubi's power from Naruto for his own dark purposes.
It could be a powerful ninja from Naruto's world who has been corrupted by the Juubi's power and somehow ended up in the Inuyasha world. He wants to use the power of the demons in the Inuyasha world to make himself even stronger and take over both worlds.
It could be a powerful Sekirei who sees Shirou as a threat to the Sekirei Plan. This Sekirei might be very traditional in their views and not like the idea of an outsider like Shirou interfering.
From the Selda side, Link could be a main character. He is used to fighting against great evils in his own world. If the Juubi were to invade, Link would be a natural ally for Naruto and the others. His skills with the sword and his ability to navigate through different terrains would be very valuable in a battle against the Juubi - influenced threats in the Selda world.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.