There could be a powerful food critic who has an evil side. He visits Ichiraku Ramen and gives it a bad review just because he wants to take over the place and turn it into a high - end restaurant. He uses his influence to spread false rumors about the ramen and Naruto has to prove him wrong by creating the best ramen ever in a big ramen - making showdown.
Perhaps a ninja who has a grudge against Naruto because he once ate all the ramen at a festival, leaving none for the ninja. So this ninja decides to target Ichiraku Ramen and tries to put a curse on the ramen that would make anyone who eats it sick. Naruto has to figure out how to break the curse and stop the ninja.
Naruto and his son, Boruto, could be main characters. Boruto might not understand his father's love for the ramen shop at first, but as the story progresses, he comes to appreciate it. Another character could be Shikamaru. He might be there to relax and have some ramen while also using his intelligence to solve any problems that arise in the shop, like a sudden shortage of ingredients.
Obviously, Naruto is often a main character since he loves ramen so much. He's usually at Ichiraku's, chatting with Teuchi, the ramen chef.
One possible reason could be that he's had a bad experience with the taste. Maybe the ramen was made wrong one day and it left a really bad impression on him.
One possible plot could be that Naruto discovers a new secret ingredient for his favorite ramen. This ingredient could be a rare herb only found in a hidden part of the forest. He then tries to convince Teuchi, the ramen shop owner, to use it in the ramen. Along the way, he has to face off against some ninjas who also want the herb for their own purposes.
Naruto is most likely to be the main character since it's about his ramen withdrawal. But his friends like Sakura and Kakashi might also be important as they could be the ones trying to help him or dealing with his mood swings due to the withdrawal.
It could be Orochimaru. He's always interested in new forms of power and experimentation. He might see Wolverine as an interesting specimen to study and try to extract his healing factor or adamantium for his own purposes. This would put him in direct conflict with both Wolverine and Naruto, who would naturally oppose Orochimaru's evil plans.
Danzo could be a great main villain in a Naruto Frankenstein fanfiction. He's always been power - hungry and secretive. He might use the concept of creating a Frankenstein - like being to gain more power for Konoha in his own twisted way, but really it's all about his own control. He could be using parts of dead ninja's abilities or something like that, and Naruto would have to stop him.
Orochimaru could be a likely main villain. He has always been interested in Naruto's power and body. Maybe he finally devises a plan to kidnap Naruto and use his body for his own reincarnation experiments.
It could be Orochimaru. He might be interested in stealing the exosuit to enhance his own powers and immortality research. He could see the exosuit as a new way to achieve physical enhancements beyond what his current jutsu can do.
Another possibility is that the main villain could be a spirit or entity that has been trapped for centuries. It uses its influence to make the Hidden Leaf Village conduct 'experiment 101' on Naruto. The spirit hopes to use Naruto's body as a vessel to be reborn into the world and wreak havoc. So it manipulates the events and people involved in the experiment from the shadows.