Though. essentially what were dealing with essentially is a lack of development as to the concept of the mod. if it was done completely all the rules and guidelines would be as you say "in the game".
This would be a reputation systems that's more robust and less plastic that it came with. As far as i know, locking the rep to the id system has been done to the fullest possibility leaving just enough leeway to either keep most the factions neutral or hostile to you within the "role" of it. Really the only wiggle room left in the id system is ticking off every npc ship possible. and even recently they've been nerfed.
Something that probably should have happened a long time ago.
Again its no ones fault per say, people in the community got what they wanted .. thats basicly the reoccurring theme here. It isn't that... the mod is broken or unfinished its just a continuous revival of features and ships factions and people have wanted in the game for years.
is she overdue for a major rework?
OH YEAH..
but that's going to take a back seat.. again to what the status quo has always been here.