A possible plot twist could be that the snake eyes are not just a power but also a link to an ancient evil. Naruto initially thinks it's a cool new ability but then discovers he has to fight against the influence of this evil within him.
Maybe the snake eyes were given to Naruto by someone who had an ulterior motive. So, as the story progresses, he finds out that this person wants to use him for their own gain. And Naruto has to break free from their control and use the snake eyes in his own way to protect his friends and the village. For example, the person who gave him the snake eyes could be working for a hidden enemy of the Leaf Village. Naruto would then be caught in a web of lies and deception, having to figure out who he can trust while dealing with the new power of the snake eyes.
A possible plot twist could be that Naruto discovers he has a hidden connection to Smaug. Maybe he is related to Smaug in some long - lost magical way. Another twist could be that Smaug is not really a villain in this fanfiction. Instead, he is being controlled by a greater evil, and Naruto has to figure out how to free Smaug from this control. It would change the whole dynamic of their relationship from one of enmity to a more complex situation where they could potentially become allies.
A possible plot twist could be that Naruto turns out to be a keyblade wielder in disguise. This would completely change the dynamic as everyone in the Naruto world and Kairi would be shocked. It could also mean that Naruto has a whole different origin and mission related to the world of Kingdom Hearts.
A possible plot twist could be that one of the Autobots is actually being controlled by an old enemy from Naruto's world. This enemy has found a way to hack into the Autobot's system and use it for their own revenge. So, while the Autobots seem to be helping Naruto, in reality, they might be leading him into a trap.
One idea could be a crossover where Naruto is transported to the world of Snake Eyes. He could learn some of the unique martial arts skills there and use his ninja techniques in combination. For example, he might incorporate the stealth skills of Snake Eyes' world into his own fighting style.
In the 'naruto has no eyes fanfiction', the plot might involve Naruto discovering a new form of chakra that is unique to his condition. This new chakra could give him abilities that he didn't have before, like the ability to sense the emotions of his opponents. There could also be a plot twist where Naruto's blindness is actually a part of a greater prophecy, and he has to fulfill it in a way that no one expected.
One possible plot twist could be that Obito was actually being controlled by a more powerful force all along. When his identity is revealed, it seems like he's the mastermind, but later it's discovered that he was just a puppet. Another twist could be that Obito has a secret alliance with a character that no one expected, like a member of the Leaf Village elders. This alliance was formed for a reason that is only revealed later in the story.
Another plot twist could be that Naruto's own chakra has an unexpected effect on the vampire. Perhaps it changes the vampire in some way, either making them more powerful or causing some sort of internal struggle within them. This would then have a big impact on their relationship as they both have to figure out how to deal with this new situation.
Perhaps Naruto discovers that Kisame has a family he's been protecting in secret, and this new knowledge makes Naruto see Kisame in a different light. He then tries to help Kisame reunite with his family while also dealing with the Akatsuki.
Perhaps the Akatsuki's neglect is a part of a much larger plan by Naruto himself. He might be trying to lull the Akatsuki into a false sense of security while he's actually gathering information or power in the background. Then, when the Akatsuki least expects it, Naruto reveals his true intentions and uses the situation to his advantage, which would be a huge plot twist for the readers who thought Naruto was just being mean or indifferent.
A plot twist could also be that Temari discovers a long - lost relative who has a dark past and tries to use Naruto's influence for evil purposes. Temari would be torn between family loyalty and her love for Naruto, and Naruto would have to help her make the right decision while also protecting their relationship and the villages.