I tried running with endeavours at the start of my campaign, but have mostly found them to be more of a hindrance than a help. I find that to be a little shame, as I am relatively fond of campaigns that focuses on macromanagement and building power and wealth.
I guess as a GM, I am not incredibly good at using it, and my players never did seem to have that sort of drive either. It was a relatively uninspired run after another, transporting this there, salvaging those ships here, building that there. So instead I introduced a powerful plot-line, which tied in with many of the characters backstories. They fought chaos heretics, stole an artefact of great power, ran away with it, got chased by the Imperial Navy, then got betrayed and chased by the Inquisition, and set out across the stars on a merry adventure for justice, and revenge. Potential things their future may hold is rescuing an Astartest strikeforce from rampaging Tyranids, siding with a radical Inquisitor whom has his roots in the backstory of one of the players, and potentially travel to an ancient world to stop the resurrection of an evil race.
The campaign has literally turned from what begun as a pretty standard RT campaign of wealth acquisition and power building, to a storyline filled with epic adventure across the stars, tradgedy and personal loss(some characters have already died along the road, and at least another is on the path of corruption), and a quest to figure out what this mysterious artefact they have found does, and why so many people are willing to see them dead over it.
I guess that's not necessarily a bad thing, but many seem to successfully play Rogue Trader as intended, with the endeavours and all. Some others play it as me, heavily story-driven. I've mostly substituted the profit you usually gain from endeavours with small boosts as they go along. Finding salvage or treasure along their way that they can sell in ports, giving them a boost of one or two points as they go. I mostly assume the hard cash is spent on various forms of investments or valuable materials they can easily carry with them.
I'm mostly interested to see how other people have handled endeavours, if they have used them extensively or if they have thrown them out of the window like I did.