Indeed, I think the Marsala character is one of the deepest in the series. He was a leader during the first Neosapien rebellion and now, ironically, 50 years later he's fighting with the Exofleet against his own kind against his brood brother, Phaeton, who actually betrayed him to the Terrans all those years ago.
He realizes that Phaeton's plans for humanity are wrong and must not be realized, but feels conflicted in stopping a war that the Terran race is responsible for starting with their own hatred to his kind.
While we see the conflict from the Human point of view as the "good guys" we ultimately know their history as flawed creatures who are not innocent in this war.
This show is deep! Way before its time and certainly doesn't get the recognition it deserves today.