In my opinion, I think there should be a more restrictive hard cap on minimum and maximum reputation hits. The particular event that brought this about was after getting in good with the Independent faction by saving multiple colonies from starvation, I bought some large weapons on the black market, which after an investigation tanked my standing by -85 to make it inhospitable. In other words, I had saved millions of the faction's citizens, but one illegal trading scandal had made them completely forget about it.
I've noticed similarly disproportionate reputation hits from being found guilty during food shortage investigation events, even when I had not caused the shortage (or alternatively, did so accidentally by buying all the food on one planet to feed a starving planet elsewhere in the same system).
On the other side of the coin, there seems to be a hard cap for positive reputation for trading -- even when relieving a starving population -- at about 50 points. It strikes me as a bit odd that killing a faction's Most Wanted Criminal can eventually raise you to 100 points, but saving millions of lives stops generating goodwill at 50 points.
So I would make a few suggestions:
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Add a hard cap on the reputation hit for investigation blame events. It doesn't seem consistent if buying 2 illegal weapons nets you a slap-on-the-wrist, but buying 10 illegal weapons gets you banned from a faction's planets entirely.
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Allow trading to boost reputation up to 100. After all, if a particular merchant handles millions of credits of contracts in a faction, you'd think he'd be able to have a little clout (campaign donations to politicians, bribery for officials, etc).
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Potentially add an option to donate (or at-cost) food during food shortage events. Players could forgo profit in exchange for a much larger reputation boost, and grant immunity to food shortage investigation events. Perhaps expanding on this idea of buying reputation, maybe each faction could have a way to be bribed. (Bribe Hegemony politicans, Sindrian Diktat junta officers, fund the construction of Luddic megachurches, offer lucrative discounts to Tri-Tachyon traders, etc). But this might be getting off-topic.