Honestly, one of the first things I would change is the dynamic between Boruto and Naruto. Naruto should not be neglecting his kids. I find it unfathomable that the young boy who lived alone most of his life and watched kids go home with their parents while he remained behind alone neglects family time. They give the reason that "The village is my whole family.", but that's nonsense with how the shadow clone jutsu works. Because all he was doing was paperwork. He could easily have a clone do that and if it disappeared then he would know and get that information from it anyway. So, Naruto would be a family man. He wouldn't be sending his clone to attend his daughter's birthday party. Not unless there was something life threatening that required him personally to be there.
Another thing I think the series missed out on is making Boruto a perfect inverse to Naruto. Naruto was a young man who worked hard to be recognized by the people who refused to do so. Boruto would be a young man who works hard, but doesn't get recognition for it because everyone expects him to be good.
Think about it. This is the son of the Hero of the Leaf, the man who beat Pain, Obito and saved the world. His grandfather is the Yellow flash and fourth hokage. His mother is the heiress to one of the most prominent clans in the village and a skilled fighter in her own right. He has every right to succeed in life. It would be weird if he didn't. I think it would be interesting if Boruto doesn't get recognition for his actions because people expect him to be good. Comments like: "As expected of Lord Seventh Son" or maybe other students mocking him thinking he doesn't work hard for what he has and relies on natural talent would be so good, because he has worked hard. He would be training everyday. Practicing none stop all to meet the height his father set, but what's the point if all he will ever be is Naruto's son? No one sees Boruto. So he stops trying and begins to resent his father because he feels like he has nothing to himself.
That is where Mitsuki and Sarada come in as good supporting characters. Both gravitate to him because of who he is. Sarada sees him as a rival who works just as hard as she does and to Mitsuki he is the sun. I also think him going to Sasuke for training makes more sense now since he's trying to deny his father in that sense. Sasuke would serve to help break that mindset and offer guidance. Having Boruto finding his ninja way would be great and in the end he'll be a legend just be like his father, but not because he is his son, but because of who he is.
The next biggest thing is that most of the arcs have to take place outside of the village, because if it does then you encounter the problem of "okay, so why didn't Naruto and everyone else not show up?" and then you have to make then do so, but you can't have them beat the villain because then they'd take the urgency from the main character. So you have to nerf them which just pisses people off tbh. So majority of the first couple of arcs would take place outside of the village.
Also I kinda like the idea of Boruto leaving the village with Sasuke, and Sarada and Mitsuki following him. Sarada wants to be and can learn a lot from her father and Mitsuki just likes being with both of them. So forming a informal Team Seven in pursuit of Sasuke could be cool. Gives us a chance to explore the rest of the world as they trail him. Cause I doubt Sasuke would be open to being a teacher at first or having people accompanying especially children.