The Evil Genius: Vulpes Inculta, the leader of the Frumentarii (spies and paramiltaries) and master strategist.
The Dark Chick: Centurion Aurelius, in charge of Cottonwood Cove. Exploring his house will reveal that he's rather eccentric for a legionary.
The Sixth Ranger: Gaius Magnus, added in the Lonesome Road DLC. Rank unknown, but probably very high since he's a beast in combat (the main Legion military works on Asskicking Equals Authority) and wears the same armor as Lanius.
Fallout: New Vegas - The New California Republic, even if viewed as good, have their leaders fit this dynamic more with their attitudes:
The Dark Chick: Chief Hanlon, leader of the NCR Rangers, the military's elite shocktroopers. Is also a Sixth Ranger Traitor, trying to sabotage the NCR to convince them to withdraw from the region, but can be talked out of what he's doing.
The Dragon - Initially General Leo, the Emperor's finest soldier and most trusted general. However, as the game progresses Kefka takes over this role, likely because Leo's sense of honor would have clashed with Gestahl's increasingly underhanded methods
The Brute - Kefka, who has no subtlety in his methods and happily resorts to Kill 'em All to solve any problem.
The Evil Genius - Cid, the mastermind behind the Empire's Magitek.