First off, I love Rogue Trader (speaking always as a
GM). I love the system, I love the freedom, the scope and the variety (for both my players and campaign ideas).
If you want to focus on political manoeuvring, gaining influence etc., have an Inquisitor overseeing them. Enforce it as part of their Writ of Trade and then make the Inquisitor a dick to attract your player's ire.
I find that whilst Profit Factor is acceptable for normal purchases, anything really valuable (e.g ship turrets, archeotech etc.) should cost them
PF.... this helps to regulate them and make these valuable purchases worth thinking about rather than (feth it, try it and we might get lucky).
Also, treat
PF as logarithmic rather than linear (your players will always game a linear one and become ridiculous e.g. we mined a full load of Adamantium for 2 Profit Factor, why not do that 30 more times for 60PF?), this also makes logical sense; beyond a certain point, more money and contacts won't make a difference to acquiring assets.
I love the management side as well. I use a Google Spreadsheet to allow the players to manage the ship. They have crew numbers, food stores, fuel stores, ammunition for weapons. E.g. their frigate could have 29,000ish crew and they had to monitor it etc. Hold on, I'll link their old spreadsheet to give you an idea.
https://docs.google.com/spreadsheets/d/1xu1BGb35CrSzZroJVPdcoOQyq6X-8MsNcuW-ewbTDd8/edit?usp=sharing
I also treat battle as more of a command exercise; equip, train and command your troops to achieve objectives for victory. For example, in one of my Campaigns, the players were once exploring an old abandoned hive city with primitives where they led an expedition into the heart of the hive with 300 Armsmen. By the end, they left with less than 70 after multitudes of traps, mass assaults, disease and supply problems took their toll.
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If you want some ideas, here's a write-up of my favourite
RT campaign (maybe I'm seeing it through rose-tinted glasses because it was my first but I still love it).
https://40kprideandprofit.wordpress.com/2016/03/09/saint-dora-the-explorer/