Re: That Rogue Trader sorta feel...
While building the ship from the ground up would take far too long, another option is that they could be repurposing a vessel, so while they would have lots of options of outfitting and shaping the final outcome, there would be a lot of choices. So more like buying (or being given) a fixer-upper than building one new.
I only GM'ed RT once, and I ran the promo adventure, it's sequel and then started in on the adventure that came with the GM's screen before the game fizzled. I altered the adventures somewhat and had lots added in to flesh them out. One of the big motivations of the game however was when they came upon a derelict cruiser rather than loot and leave, they were very intent on salvaging the ship and rebuilding it. This became an endeavor on its own, running parallel with the other main plot lines. So they first had to find a way to get it back to where it could be repaired, and then salvage and/or finance parts and labor. Their original vessel was a raider, and while they never got their crusier void worthy, it was something that motivated them to work towards.
At first I discouraged them a bit, or at least made it clear that it wasn't going to be easy to do, but when they put so much effort into it, it was clear that this is the path they wanted to pursue, sometimes more than the standard plot hooks for the adventure I was running them through. It also made void combat fun because while they wanted to defeat enemy vessels, they also had their eyes one what might be usable for their other ship.
While I have played RT the least of the four systems, I think it has the most potential for being a player driven game, and the most open to an epic campaign. I also think it would be the most difficult to run on RPoL, though I haven't had enough experience with all of the systems here to say for sure.