Perhaps the bloodline causes some internal conflict within Naruto. He might struggle with the new powers as they could have a corrupting influence, or they might be at odds with his existing ninja way. This could lead to a journey of self - discovery as he tries to balance his old self with the new powers bestowed by Shion's bloodline.
With Sasuke, things could get more complicated. Sasuke might see Naruto's new bloodline as another way Naruto is getting stronger while he struggles to reach his own goals. This could fuel their rivalry even more, or it could lead Sasuke to try and understand Naruto's new situation in an attempt to gain an edge himself.
One exciting plot twist could be that Naruto's new bloodline gives him the ability to control time. He could then use this power to go back and prevent some of the tragedies in the Naruto world, like the Uchiha massacre. Another possibility is that the bloodline makes him immune to all genjutsu, which would completely change his battles against opponents like Itachi or Madara.
One possible plot could be that they get married to strengthen the alliance between Konoha and Shion's village. Then they have to deal with political intrigues from other villages who don't want to see this alliance grow strong.
A plot twist could be that Shion turns out to be related to a powerful and ancient clan that has a feud with Konoha. When Naruto and Shion's relationship becomes known, it causes political unrest. Naruto has to fight not only for their love but also to bridge the gap between the two sides.
One plot twist could be that Naruto discovers secrets about the Uchiha clan through Minato's memories. Since Minato was Hokage and involved in village affairs, he might have known things about the Uchiha that were never revealed. Another could be that Naruto uses Minato's memories to find a new way to deal with the tailed beasts, perhaps a more peaceful co - existence method that Minato had been thinking about but never got to implement. Also, he could use Minato's memories to expose some traitors in the village who had been hidden for a long time.
One possible plot could be that Naruto, with his godlike powers, has to protect Shion from a new and powerful enemy. Maybe this enemy is after Shion's unique powers and Naruto uses his incredible abilities like instant teleportation and super - strong Rasengan to fend them off. They might also go on a journey together to find a way to completely eliminate the threat once and for all.
Well, one plot twist could be that the son has some unique power that neither Naruto nor his friends are aware of at first. Maybe it's a power that was dormant until a certain event triggered it.
One possible plot twist could be that Naruto struggles to control Itachi's power at first. Since Itachi's power is very different from his own chakra nature. For example, Itachi's genjutsu abilities might be too much for Naruto to handle initially, leading to him accidentally using it on his friends, causing mistrust among them. Another plot twist could be that the Akatsuki targets Naruto more aggressively, believing he has become a greater threat with Itachi's power. They might send their most powerful members after him, like Pain or Obito. Also, Naruto might discover some hidden secrets about Itachi's power that even Itachi was unaware of, which could change the course of the shinobi world's power balance.
It could also be a result of a unique encounter with a powerful entity. For instance, if Naruto entered a mysterious realm where the essence of Haku's bloodline was stored, and some sort of transference occurred, perhaps due to Naruto's own unique chakra nature. This could lead to him obtaining Haku's bloodline.
A possible plot might involve Naruto being exposed to some ancient and powerful knowledge or artifact. This discovery gives him the means to 'destroy' bloodlines in the sense that he can change the very nature of chakra within a person. He might use this new - found ability to break the cycle of bloodline - based power hierarchies. He could start with the major clans like the Uchiha and Hyuga, and as he spreads his influence, the concept of bloodline superiority slowly crumbles, leading to a new era in the Naruto world where a person's worth is determined by their own efforts and skills rather than their bloodline.