Huey became the Author's self insert and outside of episodes strictly centered around him, he didn't add much to the comedy.
Originally, each of the Freemans was supposed to satire a different facet of black culture - Granddad was the old civil rights movement and elderly black people, Huey was modern civil rights movement in young people (and taken to extremes especially in the first episode), and Riley was the mainstream glamour obsessed black youth.
Granddad and Riley largely stayed in those roles, but Huey broke out of his satire and was more like a passive, regular dude in the insane Boondocks world. Only in his domestic terrorism episodes did he somewhat come back to that, but otherwise he became a regular Joe in a world of absurd comedy, and while that may work in some shows, I didn't feel it worked well for Boondocks.
Riley's the best because he was always funny and he never broke his purpose