Likewise, I didn't read the whole thread, so these are perhaps my (umpteenth time repeated) opinions and ideas.
Right now, the system as it is seems a bit broken in terms of net gain of supplies verse expenditure of said supplies to regain CR. It's not impossible to gain surplus cash and buy more ships, but it is slightly challenging (not the good kind of challenge either).
Just this afternoon I tackled a large Pirate carrier fleet and had a slug fest with them. It was ugly, but I came out on top - only really lost one ship and got one frigate beat the heck up. Everything I gained in loot was sold to buy more supplies to replace what I depleted from my own stores just getting CR up to a manageable level - and that was a race to the nearest station as I didn't want to get stuck out in the middle of the system with no supplies. At the end of it I came out with 1 or 2k in profit. Not very tenable to a long play through.
Some ideas:
I do enjoy the feature of selecting priorities of repair, but I didn't notice if this was automatic or not (that is to say if the repairs and process of gaining CR was automatic). If supply distribution to prioritized repairs is automatic, as well as repairs in general, I believe it should only be allowed to start manually so the supply burn doesn't kick in immediately after the fight. Scuttling a ship based on hull integrity should yield higher supplies as well, and similarly I'm not sure if this is already the case.
In addition, I think a neat feature would be to have an industry base constantly churning out supplies. For example, if your fleet takes a planet or a station that planet or station should generate X number of supplies over the month, the process of which could be impacted by skills or investments into the planet or station. Along the same vein, repairing at a friendly planet or station should cost less supply than repairing at a backwater station in the middle of pirate territory. This gets us back into the action without having to worry too much about where supplies come from. Maybe this is a bit unbalanced, but end game it makes a bit of sense. These planets or stations could also generate aggro from pirates and raiders, and even attract mercenaries to hire. But that's a little off topic
As a side bar, I think CR readiness should be determined by more than just a generic "supplies". I would like to see ammunition, missiles, "crystals" for beams (whatever really) go into impacting the CR of weapon systems, while things like "sheet metal" or "emergency duct tape" go into effecting the combat readiness of the hull. How I see it play out is: "OK, we have no missiles, no bullets, but our ship can fly - at least we can get home and rearm." Or "Our ship is leaking personnel, and there are fires on all the decks, but we can still fire our guns!" Perhaps this is bordering too much on micromanagement, but in my opinion it adds a little more diversity to the situation post combat. As is, every situation is the same - Fight ends, you high-tail it to the nearest station to sell and buy more supplies, rinse repeat.
I'm sure I have more thoughts on the supply mechanic, but I'm at work right now, so I should probably do that.