Maybe a bloodline that gives him the ability to heal emotional wounds. Since yaoi fanfiction often deals with complex emotional relationships, such a bloodline would be quite interesting. It could be that Naruto uses this ability to help his partner or other characters deal with their past traumas and insecurities, thus strengthening their bond.
For Naruto in fanfiction, the three bloodlines could be really interesting. He could have the Rinnegan as one bloodline, which would open up a world of powerful and unique abilities like the Six Paths techniques. Another could be the Ice Release bloodline from the Yuki clan, allowing him to control ice in various forms. And finally, the Magnet Release bloodline from the Sand village, which would let him manipulate magnetic forces. These bloodlines would completely change the way he fights and is perceived in the Naruto universe.
He could potentially have a made - up doujutsu bloodline. For example, a doujutsu that allows him to see the future for a short period. This would give him an incredible advantage in battles as he could anticipate his opponents' moves far in advance. Another option could be a doujutsu that lets him manipulate the elements he sees with his vision, like being able to freeze water just by looking at it in a way.
In this fanfiction, the Sharingan from the Uchiha clan is an obvious choice. It has so many abilities like the ability to copy jutsu and predict movements. Naruto could become even more of a prodigy if he absorbs it. Also, the Aburame clan's ability to control bugs could be quite interesting. Naruto could use bugs for reconnaissance or even in combat in ways that are different from his normal fighting style. And the Inuzuka clan's connection with animals, if Naruto could absorb that bloodline, he might be able to form a stronger bond with his summons or other animals in the wild.
In such a fanfiction, one possible plot could be that Naruto is exposed to some dark magic or a powerful curse that gradually erodes his humanity. This might lead to him becoming cold and detached from his friends. He could start making decisions that go against his normal moral code, perhaps being more ruthless in battle or in his relationships. The yaoi aspect might come into play if another male character tries to bring back his humanity through a deep emotional and physical connection with Naruto.
In some fanfictions, one could be the Sharingan, which gives abilities like seeing chakra and predicting moves. Another might be the Byakugan, with its great vision powers. And the third could be something unique like the Ketsuryugan, which could have powers related to blood manipulation.
He could have the Sharingan's ability to copy and predict moves. Also, the Byakugan's near - 360 - degree vision would be really cool. And if he had the Rinnegan, he could use all kinds of powerful jutsu like the Deva Path's gravity manipulation.
One interesting combination could be the Uchiha bloodline with the Uzumaki bloodline. The Sharingan from the Uchiha and the massive chakra reserves and sealing abilities of the Uzumaki could create a really powerful Naruto. Another could be the Hyuga bloodline combined with the Uzumaki. The Byakugan's visual prowess along with the Uzumaki's chakra would give Naruto enhanced perception and more chakra to use for powerful jutsu.
One possible plot could be Naruto suddenly awakening all bloodlines and using them to defeat a new, extremely powerful enemy that threatens the entire ninja world.
One possible reason could be Naruto's internal conflict. In yaoi fanfiction, the relationship is often complex. Naruto might be running away because he's confused about his feelings for Sasuke. He may not be ready to face the intensity of the relationship that the yaoi concept implies.
It's just a wild concept in yaoi fanfic. Maybe the author wants to explore the extreme of relationship dynamics and gender - bending ideas. Since it's fan - made, there are no real - world rules to limit it. They can create a whole new set of rules within their fictional story to make Naruto pregnant, like introducing some super - rare jutsu that can change a male's biological function.