So once our current Deathwatch campaign is wrapped up I plan to run a Rogue Trader game with my 3 core players. However all of them have their hearts set on their current character ideas, a Seneschal, an Ork Freebooter (eventually becoming a Big Mek) and a Dark Eldar warrior (once the Soul Reaver comes out); now I think this could be interesting and I don't have a problem with it but it does bring up an obvious problem, the Rogue Trader will have to be an NPC.
This presents me with an odd issues; preventing the commander of the operation from stealing the spotlight from the PCs. I'm thinking of leaving the RT physically crippled at one point (I won't have him start that way, he will gain Exp at the same rate as the party and it makes little sense for a RT to start a career while he's physically unwell) and thus relegated to ship command and mission control so to speak. However this still leaves the fact that an NPC will be giving the main orders (players will obviously have their own side agendas and get control of HOW they go about their missions, plus I am characterizing the RT as a man who is willing to delegate when its called for) in a game where I feel that the appeal is the freedom to go out into a huge sandbox and make your own fortune.
In a nutshell my question is; how do I keep the Rogue Trader relevant to the story without having him (and thus me as the GM) have total control and assume a role similar to a Inquisitor/Watch Captain/etc in other games? I'm basically trying to avoid making this into "Deathwatch/Dark Heresy with space battle mechanics" in that player characters are given orders that propel the plot rather than opportunites to seize; because in the end its the Rogue Trader (normally a PC who would consult out of character with the rest of the party) who makes the final decision.
I guess I could take the easy route and make him a push over but I doubt my players would find that compelling or believable.