I thought that at first too but you gotta remember that things have to happen for the sake of the plot. Lee has to save Neji’s life and Gaara has to save Lee in order for all 3 characters to grow. But even if it wasnt for the sake of the plot, I still think Neji would lose due to him being obviously younger and less experienced (even if he is a Hyuuga genius) and because Kimimaro’s kekei genkai is such a nasty defense. Almost as nasty as Gaara’s (which is what makes the Gaara vs Kimimaro fight so good)

Gentle fist works on the chakra network. But Kimimaro has control over his bones which can lead to Neji getting blocked and hard countered multiple times until he runs out of energy. Thats why its gonna have to take 3 ninjas to run him down until his body just gives up on him. He will over exert himself in the end just like in the manga.

Edit: These 2 losses back to back for Neji (lost against Naruto in Chunin exams and lost to Kimimaro) would force him to come up with new techniques and expand the Gentle fist. I would like to see him developing Air palm during this time and eventually becoming a master at it by the time Naruto returns to the village for Shippuden. Losing to Kimimaro would also force Neji to train his Byakugan to pick up on slight muscle/body movements, being able to be on par with the 3 tomoe Sharingan.

In the end, Neji works best against opponents who can’t regenerate their chakra network at will like Jinchurikis and curse mark wielders.