I don't think I'd call Goku a genius in combat. A genius in training might be accurate, but I don't want to get too far off topic.

What we're seeing is a transition that should have taken place over the course of the entire series taking place in a few chapters. Naruto should have shown a bit of improvement after every battle. He especially should have improved during that training with Jiraiya. Since he hasn't improved as much as he should have in all that time. Kishimoto is playing cath-up. It's a shame, but he does need to improve a lot for the plot to advance.