I've made account just to post this

I think the idea behind this mod is great. Bonuses are not overwhelming yet make me stick to my ship longer. Also makes it more unique, as it may lead player to upgrade ones ship to play into reputation strengths.
I downloaded the 1.2.0 BETA and here is my feedback thus far:
NOTE: I don't understand exactly how various things are calculated and I base following observations on the way things felt when they happened. It is entirely possible that things work differently, I just couldn't tell.
1. There are some weird interactions with, possibly, Ruthless Sector? Something to do with how battle difficulty is calculated or XP is handed out post battle. I fight non-stop against fleets that have numerical superiority (ie. 1 me vs 10 ships) and somehow I cannot break past combat rating of 65% in my destroyer. Seriously, I pulled 2 cruiser kills + 7 frigates with a single destroyer and my rating went from 65% to 67%. In previous version I had no such issues and went past 70% easily. I cannot imagine what kind of odds need to be stacked against me to go up to 90% right now.
2. Combat rating system as implemented punishes hit-and-run tactics, as it cannot distinguish between orderly retreat and total defeat. Basically the only way to rise it is to go in enemies face and nuke it out. I did two runs against one huge convoy and even though both times I pulled out with around 20-30% hull (and many kills), my rating went down from 65% down to ~50%. I got entire convoy third time. Went up to like 53%? I mean I just killed smth like 20 ships with a single destroyer. Give me some cred

3. Does hull damage affect battle combat rating? It seems to do so and tbh I don't think its good idea. Battle performance is already measured by number of kills/damage player manages to deal and it punishes armor ships that always end up with some hull damage. As a result fast and maneuverable shield tanked ships get much higher CR.
4. While not necessarily a bad design choice, some reputations are game changing for given hulls and some are not very useful. Ie. basic 4% of Strong Armor on puny destroyer with paper thin armor vs same bonus on Onslaught... 3% of Strong Engines on same overdriven destroyer? Frigate killer.
5. Current system punishes pirate play style a lot... like, I hunt smugglers, trade convoys etc. to get supplies when in hostile territory or when non are available and every single time my combat rating goes down because I pick on too easy targets... which forces me to attack bigger convoys... which I need to raid several times to chip down annoying ships... which lowers my CR even more... you see where this is going

6. Right now I am not even sure how lost in combat rating is calculated, but I went once against hegemony fleet detachment (solo, they bounced off Hyperspace Storm and got me) and while I cleared all frigates and destroyers while under heavy fire from cruisers and capitals... I got -7% to CR... like seriously? Haven't I just done something epic? If I would do the same thing without hundreds of Pilum missiles flying around and won, my rating would go up.
Suggestions:
1. Ignore hull damage to ship when calculating score for won battle.
2. Factor in hull damage to ship when calculating score for battle from which player retreated (would work nice with hit-and-run), so that i.e. if 0% hull damage then CR penalty for losing would also equal 0%.
3. Lower player combat rating for lost battles based on actual number of ships lost.
4. MAYBE only battles that can rise combat rating can also affect it negatively? I mean, I get that - killing small smuggler fleets is nothing glorious, but cruising around and around just to find the fleet of right size is just not fun.
Edit:
I noticed how difficulty is calculated in Ruthless Sector and now I see what was the problem with point 1. What got me was that "1% per player level factor in calculation of player's fleet strength. Since I fought 1 vs 10 from the very start, I got ton of XP and raised my character level super fast to almost level 30, so for the purpose of strength calculation I got 30% stronger.
Also, when I look at my fleet strength evaluation I also think that your mod counts player level twice. Once as that "1%" and second time as "2.5% per officer level" when strength of individual ship is calculated.
Now tell me if I am wrong, but I don't think that even level 50 player in frigate is going to contribute to a fight as much as a carrier, but according to the formula he would add more fleet strength. Unless, everything went into "fleet" skills. I can see why it was done that way, however it not going to work in all situations. Luckily its very easy to tweak in settings

Amazing mod!
I would suggest adding some more text to FAQ, ie. "If you enjoy playing small, you might want to change the [setting] to [something]".
Edit 2:
Further reading also allowed me to deal with point 6... kinda. There is this "maxBattleDifficultyEstimation" set at default to be 2.0. I think you put a limit, so that even super impressive victory would not catapult player up to level 20 or higher in one go? Now this will also limit how your combat rating is going to rise from same victory, wouldn't it?
Is it possible to add another factor in xp calculation? Like "whatever XP I get... multiply it by 0.5". That way I can make impressive battles to have more impressive impact on ships' reputation, but by lowering overall XP by a factor of XYZ, prevent suddenly becoming too high level frigate pilot.