If I were to guess, not knowing any of what goes on behind the scenes, it's because of a lack of an agreed upon vision at the outset of a director coming on board. The director might be given a long leash at the beginning to do what they want until it interferes with the apparently stringent parameters set up by Kennedy and the rest of the brass. If there was more clarity in the early stages of a production, more vetting when it comes to personality and exactly what the person intends to do with the film, I don't think this game of director musical chairs would be happening. So it does come down to Kennedy and the other higherups. The onus is on them to hire the right people and communicate what the "right people" even are.
Their original plans of hiring a different young talent for each film had merits. Would keep the franchise fresh by constantly drawing in young blood. However, they probably didn't expect those visions to end up clashing so much. She was supposed to be the new Lucas but the problem's that she's not storyteler, she's just a very talented producer.
They now seem to have put J. J. Abrams and Colin Trevorrow as the "showrunners" of the main storylines going forward. Sort of acting as the new "George Lucas". I frankly think that might help things going forward. This way, these stories maintain a certain artistic vision that's already proved to work for them in the past.
I wonder how much influence The Book of Henry had in getting Trevorrow booted. I'm one of the few people who went to it in the theater. The movie is competently (if not spectacularly) shot and edited, and well acted, particularly by Jaeden Lieberher. What's made it notorious is the absolutely PREPOSTEROUS plot developments later on. We're talking some really silly stuff. It's mostly revealed in the trailer, or you can at least infer most of the movie from it. Despite that, the movie has some crazy charm, almost like a mid- or higher-tiered Shyamalan film where you like it despite its stupidity. Trevorrow's Safety Not Guaranteed wasn't very good, and Jurassic World was totally average, so that combined with the weirdness of this movie probably decided it for the producers.
Safety Not Guaranteed is 90% Certified Fresh with an average score of 7/10 on Rotten Tomatoes so critics thought it was good. So I doubt that film played any part in him leaving Episode 9. And despite Book of Henry being shredded by critics it was a small budget film and was a Focus Feature film. Next to Jurassic World's insane success Book of Henry is a total non factor. If Disney was judging him based on his previous work, JW would have been what they were focusing on.
The most likely reason he walked away is he couldn't crack the story. After Fisher died they had to throw the Episode 9 plans in the garbage, because Leia was supposed to play a big role in Episode 9. They kept calling it her film prior to her death. So when Fisher died they brought in a new writer, Jack Thorne, and started working on the story without Leia. Either what Colin and Thorne delivered wasn't to Kennedy's liking or they just weren't making any positive progress. Considering what Thorne did to Harry Potter and the Cursed Child I really don't have a hard time believing that Thorne and Colin delivered something that Kennedy didn't like. And there are reports that Colin had let his JW success go to his head and his ego was causing problems.