I apologies in advanced as this will likely be a mess as i rewrite it hundreds of times and snip parts back together, this idea is also to go with my previous post about the Galaxy gen change, but can also fit in the current gen system.
Currently when travelling though the system, you can get a quick idea of whats travelling around you, grey IFFs travelling in a straight line between stations and the relays are civilian cargo ships, ones that are not will be patrols, and all red IFF's will be pirates who will attack you immediately when within a certain range, IFF's always being red can make sense for target bounties when your given a detailed location (Though having some fugitive bounties where your not given a precise locations could be interesting), however for things like the roaming pirates it make less sense, they would want to stay hidden, IFFs could work in a way where AI and you can turn off your IFF and "run cold" this will lower your signal detection range however will also force your ship to be slower (could also lower how far you can pick up other pings though that might be too much of a punish meant) this will not only allow for some low tech stealth as a more high tech option cloaking, is already planned, this will also spice up the ambush mechanic that is planned
Being around faction ships with your IFF off could also allow for new ways to interact with the factions, having your IFF off within "civilised" space will come with a fine, depending on your relations with said faction they might charge you more or less, maybe even with low enough of a relation they will assume you to be a threat regardless, or even being in higher combat systems
Having your IFF off can also bring in new trade and mission types, everyone love to smuggle illegal goods, though maybe being impossible with the proper factions (Monolith, Imperium and Cabal) Fringe and maybe a new type of station "black sites" or pirate bases or something similar would be more open to illegal trade however might be pushed to still uphold certain laws mainly Fringe
Trade on the Black Marker can lead to cheaper prices on certain regular goods, a set amount however as to not abuse simply always buying low at illegal ports
A possible way to trade with "civilised" stations could be through missions, there could be a cargo ship hiding somewhere close to the station that you trade with, this however could also be an ambush if it is the reward will be in whats salvaged, with either the cargo ship itself holding valuables, or the attacking ships
Sensor also currently feel a little off only really being used on kitting ships to fully use the potential of their range, though a more odd change, rather then just extending your sensor range, it shows outlines of objects outside of your visual range, this can help with countering ships running with their IFFs off but also help when in dense clouds, this could open up to traversing through systems with dense nebula, maybe even add in a new type of system, a young system with a red dwarf at its centre and a dense dust cloud completely encompasses it with many large asteroids and a bunch of small proto planets but no gas giants