I like the puppet captain, too…. which gives me an idea:
What if the rogue trader was a woman, who is mortally wounded while pregnant. The tech-priests manage to put her into suspended animation before she passes which, while it will not save her, will save the baby - the last remaining heir of the dynasty.
The problem? Well, suspended animation means that the child will not develop and if they remove the captain from the stasis field the baby dies along with the Rogue Trader dynasty.However, due to some Xeno-tech / archeotech engineering, the tech-savants find a way to affect the development of the child's mind. While the they are unable to find any way to safely remove the unborn child, they begin an accelerated education and hypno-indoctrination program in which much of the previous RT's memories and knowledge becomes infused with it's mind.
As a result: the dead puppet captain remains entombed in the captain's throne on the command bridge as a life-support system for the Rogue Trader Brain-Captain.
Would also be perfect: the RT has no agency, and only a very limited and unreliable way of communicating with the command crew. In many ways, the brain exists only as a repository of knowledge which the Seneschal (and tech-priests) know how to access. It could be that this situation has persisted for months, years, decades or even centuries. It's almost like some sort of Oracle, guiding the destiny of the dynasty but not actually in charge of anything.
While it might offer counsel, the 'Captain' has no way to interact with the outside world (unless it develops psyker abilities but that would raise a whole other mess of issues…). That means that the Seneschal is nominally "in charge until the captain is fit to assume command of the dynasty." Of course, whether the Senescal decides to actually set out to search for the technology that might allow the tech-priests to safely remove the captain-brain from the Rogue Trader's body, or just sets out to make themselve rich is up to them… It also means that as a GM you can use the voice of the Captain to make suggestions and requests but that the PCs are under no obligation to follow them, or even acknowledge them. In fact, the Captain-Brain's requests might completely mad - how else can you describe its situation but maddening?
Would be the type of game which would work really well with 'Xenon crew members' and a Renegade Navigator or three. A dirty Arch-Militant 'secirity officer.' A borderline Heretek Genetor Explorator. After all, something like this has got to be heretical and at this point, what's one more freakshow? I'm sure this ship would be ripe for mutiny and massive political intrigue.
Sounds like a fun time in the making!