A new character could be created as the main antagonist. For example, a powerful sorcerer from a far - off land who has come to Hyrule seeking its magical energy. He wants to use the power of the Dragon Knight to open a portal to a realm full of dark magic.
Perhaps an ancient evil that was sealed away long ago has been awakened. This evil takes the form of a shadowy figure and has the ability to possess other beings. It targets the Dragon Knight because he has the power to stop it from spreading its darkness across Hyrule.
Death itself could be the main antagonist. It could be a force that doesn't have a physical form at first but starts to possess characters or objects in the Zelda universe. For example, it could possess Ganon, making him even more powerful and malevolent. Or it could be an unseen presence that is slowly draining the life out of Hyrule, causing plants to wither and people to fall ill.
There could be a rival kingdom led by a tyrant king. This king sees Naruto's village as a valuable asset and wants to conquer it. He has a large army of knights and foot soldiers. His knights are well - trained and equipped, and he uses underhanded tactics to try and defeat Naruto and his comrades in battle.
Maybe a group of dark wizards who are jealous of the power of the dragon knights. They form an alliance to destroy the dragon knights and anyone associated with them, making Harry and his newfound friends their main targets.
One idea could be the Dragon Knight having to form an alliance with a group of misfits to defeat a powerful dark wizard. They could each bring unique skills and personalities to the group.
The World Government could be the main antagonist in a more complex way. They could be secretly manipulating events to pit Dragon and Luffy against each other. For example, they could spread false rumors about Luffy being a tool of the revolutionaries, which would make other pirate crews and kingdoms target him, and at the same time make Dragon look bad for having a son who is causing so much chaos. This would force Dragon and Luffy to either fight each other or find a way to clear their names together.
One option for the main character is an OC (original character) who has the spirit of Naruto inside him but looks like Link. He has the determination of Naruto and the adventuring skills of Link. In the harem, we could have Ino from Naruto. She's confident and has her mind - related jutsus. And from Zelda, Midna could be a part of it. She is a complex and powerful character. Another character could be Hinata. Her shy yet strong nature would add an interesting dynamic to the harem.
Perhaps a jealous wizard. He was once friends with Astrid but when he sees her gain the power and beauty of a dragon, he becomes envious. He starts to cast spells to make Astrid's life as a dragon difficult and tries to steal her new - found powers for himself.
It could be a power - hungry wizard who wants the dragon for himself. He might try to steal the egg from Jon before it hatches or take the newly - hatched dragon by force.
A powerful and corrupt World Noble could be the main antagonist. They might be trying to stop both Luffy and Dragon's efforts for freedom. The World Noble could have a large military force under their control and be causing chaos and oppression in various parts of the world. This would force Luffy and Dragon to join forces to take them down.
Another option is a rival dragon slayer who sees Natsu's transformation as a threat to his own status. This rival could try to stop Natsu from fully becoming a dragon or try to defeat him to prove his own superiority.