Well, seems I missed a bit while at work. Let's see here...

I think going Rogue Trader would kinda be its own theme, really, well apart from Imperial Navy. Like JB said, its more a mixture of Inquisition (with a more radical bend typically) and Guard/Navy than anything else. While Rogue Trader games can be fun, I figure this would indeed be better suited as an actual Imperial Navy expenditure, probably with a good deal of oversight/interfering from our good friends at the Adeptus Mechanicus. Either run Rogue Trader or this, I figure, would be better than shoe horning Rogue Trader into this. Just my two cents there, though, I'm still in regardless on that.

As for being part of a battle group, I think we could cater to both sides here. Folks who want to stay focused on one ship, bridge staff for the main vessel. Those who want their own ships could either be launchable void craft from the ship (Solves the interaction between fights) or full blown escort class vessels independent of the main ship. I would lean much more towards the centralized ship instead of many individual captains, but again, just my two cents.

And W40k names are indeed, as they say, bitching.