As I like posting up my plans for bad guys/NPCs for upcoming games, here's a pair for a Rogue Trader game - the brothers Tiberius and Agamemnon Varran-Delin, Twin Scions of the Varran-Delin Dynasty.
A man with the temperament of a Fenksworld Pit Thing (and a face to match), Tiberius was a military man before the Warrant of Trade came to him. His father, Galanius, had sent him to serve with the Imperial Guard (where his status and wealth drew him no end of criticism and veiled threats). However, Tiberius proved himself to be a resourceful soldier, a powerful combatant, and in time a great leader of men, becoming a General in but a few short years (many suggest he obtained a few "field promotions" in his time in the warzone). Numerous engagements fought, battles won, and accolades received later, he got word that Galanius had passed away, and left his considerable fortune (and Warrant of Trade) to his son.
After finishing his final campaign (prying a small patch of the Expanse from the Traitor 46th Allanian), he returned to Port Wander to claim his Warrant of Trade, only to find a usurper in his place - Agamemnon.
Where Tiberius was strong, cautious, and violent, Agamemnon was effete, proud, and hedonistic. Raised as a merchant on a Noble World, Agamemnon already had a fair fortune under his belt - but the Warrant would provide chances for more riches than even he could spend. When the news came of Galanius' death, one of his Adepts found a link to the dynasty within the hour - and within a second hour, Agamemnon was on his way to Port Wander to claim his title as Scion of the Dynasty.
Turns out, Galanius had played away from home a fair bit - and, due to several quirks in the wording of his will (possibly intentional), both men had an equal claim to the Warrant. After many weeks of deliberation, legal wrangling from both sides, and more than a few threats of violence, both men decided to share the Warrant - each a full Scion, and possessor of half the total wealth of the Dynasty (Agamemnon is still bitter that he had to pool his assets with the Dynasty, feeling that Tiberius had infinitely less to offer).
Both compliment each other incredibly (though neither will admit it) - Agamemnon providing a "face" to the operation, dealing with the trade, barter, and political side of running a dynasty, while Tiberius is the man for battles, planning expeditions and campaigns, and acting as the personal intimidation that a Rogue Trader requires. This synergy of skills makes the two a dangerous combination of brawn and brains - but there are ways to drive a wedge between them...
The Varran-Delin dynasty has several businesses up and running, and a few more on the backburner when the PCs encounter them. The "own" a small agri-world, Cassas III, on a backwater Warp Route in the Expanse, where they export food, livestock and materials to several nearby Hive and Forge Worlds, making a tidy profit as the only agricultural planet in the system. Agamemnon is also known to sponsor gangs on one of the system's Hives (Hive Belarius), in order to run another small profit from drugs and weapons smuggling. While he is not yet "the man behind the throne" on Belarius, it's certainly enough to give him considerable control of the populace. They also have several successful trade routes dotted through the Expanse.
By which I mean, what they can pull from their back pocket at a moment's notice.
Agamemnon's Hive world links mean he has a steady supply of smugglers, unmarked and hard-to-trace assassins, and even the odd starship at his beck and call. He also has a few more unusual contacts, including a mysterious Eldar Corsair who seems to owe him a favour or two.
Tiberius, on the other hand, can call upon his previous rank and standing, gaining access to military hardware, manpower, and in a few rare cases, detachments of Space Marines and other highly-regarded members of the Imperium.
I might have set these two up as antagonists, but they're most certainly not villains - they are simply rivals to your Rogue Trader line. They could become somewhat terse allies (for example, you are both racing to reach a certain planet, when you are besieged by Orks/Eldar/Chaos, or even another Rogue Trader), or you could figure a way to destroy their dynasty from within (remember, Tiberius thinks Agamemnon has no real right to the Warrant, and Agamemnon is pissed about having to share his money with his "brother") - old rivalries could be forced to come to a head, all with a well-placed word or a diversionary attack - I imagine less scrupulous Captains might order an assassination attempt on one or both of them, and try and pin them on the other brother.
Agamemnon might also turn traitor - after all, he's just a few dick-tentacles away from being a Slannesi cultist, what with the hedonistic attitude and "unusual" tastes. Would you be willing to team up with your rival to take on his own brother? Would handing him over to the Inquisition ruin Tiberius's reputation?
Even Tiberius could be your villain - Agamemnon fears that he's becoming too brutal with his methods, and wants you to help take him down. Problem being, Agamemnon cannot be seen to be interfering - the fallout from the two brothers openly warring could be disastrous for their House. This works best if the PCs are a small, foundling dynasty - were they more powerful, they might simply allow the battle to run its course, watch as Agamemnon or Tiberius fell, and the other left in disgrace, and move in and clean up, sweeping trade routes and interests right out from under them. Of course, that could be just the plot you wanted to run...
Characters to reference - King Leonidas (300), any cowboy played by Clint Eastwood, any generic "Badass Leader" type.
For game stats, make him a proper physical challenge - a powerhouse in a fight, with high WS, BS, and Ag, possibly to the detriment of his Fellowship. Intelligence should be decent, and his Willpower should be near-legendary.
Characters to reference - Littlefinger (ASoIaF, Game of Thrones), Lucifer (Sandman/Lucifer), Xilius (Dungeons and Dragons: The Abominat... I mean, Movie), any "Magnificent Bastard" character.
In-game, he should be a character defined by Fellowship skills, like Charm, Deceive, Barter, etc. In a straight fight, he will fall - though he always has a few dirty tricks up his sleeve, and a personal guard equipped with the best money can buy.