Neji isn't the only one who changes at a potential loss.

Gaara loses his ability to chase twice going from 1 to 2 stars but gets stronger powers.
Sasuke gets a more expensive jutsu and loses the Curse Mark ability in exchange for more combo power.

There's others I'm sure as well but not every character is a straight upgrade. In fact two years ago when I played this game in another version it was common meta to NOT upgrade Sasuke because 2-star Sasuke worked better with certain combo teams at the time.