Well, there's a fanfiction called 'Kyuubi's True Form'. The plot twist here is that the Kyuubi has a completely different true form than what was expected, and this form has different powers and a different relationship with Naruto. Also, in 'Naruto's Lost Kyuubi', Naruto suddenly loses the Kyuubi for an unexpected reason, like a time - travel accident, and he has to find a way to get it back without his usual power source.
One interesting plot twist is in 'The Kyuubi's Sacrifice'. Here, instead of Naruto having to control the Kyuubi, the Kyuubi sacrifices itself to save Naruto from a powerful enemy. This flips the typical dynamic. Another is in 'Naruto and the Kyuubi's Mind Swap'. They swap minds, which leads to hilarious and also very deep moments as they have to understand each other's lives from the inside out.
One interesting plot twist could be that the sealing process goes wrong in a completely unexpected way. Maybe instead of just sealing the Kyuubi's chakra, Naruto accidentally fuses with it on a spiritual level, giving him new and uncontrollable powers at first. Another could be that during the sealing, a dark entity from another dimension tries to interfere and take over the Kyuubi's power within Naruto. It would add a whole new layer of conflict and mystery to the fanfiction. Also, perhaps the seal actually has a hidden purpose that was set by an ancient force long ago, and as Naruto discovers bits of this, it changes his understanding of his role as the Kyuubi's host.
One popular plot twist could be that as a female Naruto born as the Kyuubi, she has an even stronger connection to nature. Maybe she can communicate with the forest spirits in a way Naruto in the original couldn't. This could lead to new alliances and powers. Another could be that her female identity causes different reactions from the villagers. Instead of just fear and hatred like Naruto faced, there could be a mix of awe and jealousy, which would change her relationships and how she grows up.
One interesting plot twist could be that the symbiote actually has a mind of its own and tries to take over Naruto completely, but the Kyuubi's chakra interferes and creates an unexpected alliance between the three. This could lead to Naruto having new and strange powers that no one has seen before.
One interesting plot twist could be that in the fanfiction, the fem Naruto in the Kyuubi suit has the ability to communicate with the spirits of past Jinchuriki. This gives her an edge in battles as she can learn from their experiences. Another twist might be that the suit itself has a mind of its own and sometimes takes over to protect Naruto, even if it means going against her own wishes temporarily.
One plot twist could be that the 'pregnancy' actually turns out to be a way for Kyuubi to transfer its remaining power to Naruto in a more permanent and extreme way. Instead of just lending power, it's like a total fusion of their essences. Another could be that the 'pregnancy' is a ruse by an enemy who has manipulated Naruto's connection with Kyuubi to make it seem like this is happening, when in fact they are trying to steal the power that would be created from such a union.
Well, in some 'Naruto corrupted by fem Kyuubi' fanfiction, a great plot twist could be that the fem Kyuubi is actually a part of a larger prophecy that Naruto was unaware of. The corruption she brings is a necessary step in fulfilling this prophecy. It could also be that the fem Kyuubi's true form is not what it seems, and when Naruto discovers this, it completely changes his perception of her and their relationship. For instance, she might be a reincarnation of an ancient and powerful being, and her 'corruption' of Naruto is a way to awaken his latent powers related to that ancient being.
Another aspect could be that the Kyuubi is being controlled by a hidden force when it kidnaps Naruto. This hidden force might be using the Kyuubi's power to start a war between the village and other hidden villages. They could be framing the Kyuubi to create chaos, and Naruto, being the jinchuriki, is the key piece in their evil plan. Naruto might then have to figure out a way to break free from the Kyuubi's hold and expose the real villains behind the kidnapping.
One interesting plot twist could be when a Splatoon character suddenly gains Naruto - like powers. Imagine an Inkling being able to use the Rasengan. It completely changes the dynamic of the story.
A really interesting plot twist can be when the characters from Undertale end up in the Naruto world and they have to adapt to the ninja way. For example, Sans using his shortcuts in the middle of a ninja battle, which throws everyone off guard. It's unexpected and adds a whole new level of humor and chaos to the story.
In some fanfictions, a big plot twist is when Naruto suddenly gains a Devil Fruit ability, completely changing the power dynamics. For example, in 'Naruto's Devil Fruit Adventure', he gets a powerful fruit that makes his ninja skills even more formidable.