There could also be a new character created specifically for the fanfic. This character could be jealous of Naruto's second chance and the fame he had in his first life. So, this new antagonist tries to undermine Naruto at every turn and stop him from achieving great things in his second life.
It could be a rogue ninja from another village who has a vendetta against Naruto for his past actions in his first life. This ninja might see Naruto's second chance as an opportunity to finally get revenge.
The main antagonist could be a corrupted version of Naruto himself from an alternate timeline. This 'evil Naruto' has different ideals and is bent on ruling the ninja world with an iron fist. In Naruto's second life, he has to not only face this powerful version of himself but also figure out how to stop his own dark tendencies from emerging.
It could be Orochimaru. In this fanfic, he could be a player of the same 'life - game' as Naruto, but with a much more sinister goal. He might be trying to manipulate the game rules to his advantage, like finding a way to make all the ninja in Konoha his puppets. Naruto would then have to figure out how to stop Orochimaru's evil plans within the game - like mechanics of his world.
Perhaps an old enemy of the Hidden Leaf who has resurfaced and is specifically interested in stealing the secret behind Gear Second. They could be a powerful and cunning foe, using various tactics to get close to Naruto and figure out how he activates and controls this power.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.
A new character could be created as the antagonist. For example, an Uchiha who has been corrupted by the power of the Sharingan and wants to use Naruto's special Uchiha - related abilities for his own evil purposes. This character could be jealous of Naruto's unique position within the Uchiha - related story and try to take it from him.
It could be a rogue ninja who has mastered parkour to an extreme level. He uses his skills to steal important ninja artifacts and Naruto has to stop him. This antagonist would be very fast and agile, making it difficult for Naruto to catch him using normal ninja techniques.
Madara could still be the main antagonist even in a 'naruto bankai fanfic'. He senses Naruto's new power and realizes it could be a threat to his plans of world domination. He adapts his strategies and attacks Naruto with all his might, trying to prevent Naruto from fully mastering and using his Bankai - inspired power to its fullest potential.
A powerful and corrupt ninja from another village could be the main antagonist. He hears about the unique knives in Naruto's village and decides to steal them to increase his own power and the dominance of his village. He would stop at nothing to get his hands on these knives, even if it means starting a war between the villages.
A mysterious figure within Konoha who has a hidden agenda. This person doesn't like the idea of Naruto breaking the norms and wearing a dress. They secretly manipulate events to make Naruto's life difficult while he's in the dress. For example, they might arrange for Naruto to be in situations where his dress - wearing causes maximum embarrassment, all in an attempt to make him conform to the traditional ways.
It could be Orochimaru. He has always been interested in the power of the dead and bringing back the strong. He might have found a way to reanimate Naruto for his own evil purposes, like using Naruto's power to take over the ninja world.