I am sure someone has though of this before, but tariffs should be tied to faction rep. The higher your rep at that market the lower the tariffs should be.
Another thing I would like to see is the ability to bribe your way into an open market after coming in secretly. This would let you get full reputation for trading there "openly" while still letting you come in secretly. Maybe instead of seeing a greyed out "open market" button you instead got a "talk to the port authority" button instead. That would open up a interface that lets you talk to the various station administrators and lets you offer them bribes. Some would be more loyal than others (to either you or their faction), and your individual reputation with them would also impact the price and success rate. Successful bribes would build your rep with that administrator, but not with the faction. This means you could be super friendly with an administrator, even if you are at war with that faction. A failed bribe would immediately alerts all faction fleets in the vicinity of your ID, almost like you had just flashed your transponder on and off.
Expanding on the market access thing (and also something I suspect has been suggested), we should have a way to spoof our transponders, setting up alternative IDs. I am not sure if the best way to balance that would be to require a "spoofer" module on each ship, or if it should be a fleet level skill for the player, but the general principle is you would have access to a number of different IDs to build reputation under. There would always be a risk that these IDs would get associated, with negative reputational consequences, but this would let you maintain the ability to trade with factions your real ID was not on friendly terms with. This would obviously need to include things like being able to see the reputation of each ID with all the various faction, and which IDS they know are associated with each other. Such a mechanic may even allow you to spoof IDS that belong to a specific faction, letting you seed hostilities under a false flag (though it should obviously be very difficult and unreliable to get and use such IDs).