Since Palpatine's not really a chessmaster with the villains (only manipulating things with the Republic, nothing more) both my central antagonists represent that aspects of the Mandalorian Coalition.

The lead big bad is the female general of the Mandalorians. Deadly, and remarkably experienced, but there's also hints of something deep with her with suggestions that the invasion of the Republic is really a last effort to head off the Mandalorian's complete entropy and extinction, because from their standpoint its either defeat the Jedi and re-solidy their place in the galaxy, or go down fighting in defeat.

The other big antagonist is a former major crime lord who commands the clones of the raw infantry. In a character sense, he's a much darker version of Han Solo: a rogue and charming in his own way, but also completely and utterly ruthless about his goals. While the Mandalorians and the Criminals/Pirates are technically in an alliance, both don't really like each other, but need one another in order to take out the Republic and the Jedi.

Mandalorians bring the cloning technology and experience against the Jedi with the criminal powers providing the manpower for cloning and knowledge of the Republic's weaknesses. Its an enemy that can differ enough from the Empire to provide a contrasting villain while still being a large enough threat to provide tension.