Another issue that Ikemoto has to deal with is the unpopularity of Nail/Kawaki.
In Part One, he was one of the most powerful and competent person in the main cast, with only Madoc and Bolt being able to come close to him. Completely outstripping the rest of the cast due to the favoritism Ikemoto bestowed upon him. As well as ultimately being the focus and core of the story Ikemoto was telling.
In Part Two, he is the biggest Jobber of the entire cast, possibly the worst I have ever seen in a story, constantly losing his fights and screwing everything up. It is even implied that some of the cast besides Bolt are stronger than him, at the very least Cups. As well as, instead of being the focus of the story who is making most of the decisions; it is more the cast is working around him. So he doesn't interfere and make everything worse.
Now you could justify it in story. His decline in power is because unlike everyone else, he doesn't have a dedicated mentor to train him. So while he didn't stagnate entirely, he didn't improve as fast as the rest of the cast. For his decline in competence, it is because of the guilt and stress of blaming Bolt for Naruto's "death," trying to kill him to cover it up, and an obsession with destroying the Otsutsuki within him to justify his actions.
But It is more likely, that during the break between part one and two. They went through the data and realize Kawaki was too unpopular to have such importance in the manga. So his importance in the story has been reduced drastically. So what happened to Sakura but this time it is the actual data instead of skewed numbers to make Hinata the heroine. Oh, the irony.