Back to the topic of supplies, seeing the settings next to each other makes it obvious why players were feeling the pressure on their wallets -- there's such a wide difference from what they're used to.
That said, I like Castrin's idea of making in-dock repair more expensive. That way, even if you use all your spares in a mission, you are still going to have a mean repair bill because hull is not repairable. If a smaller ship is able to beat up a bigger one enough even in a losing cause, it will be a moral victory just being able to cost your opponent some dough.
We can't go back to 8 spares max, because it is not a settings-controlled variable, but a code change. So, we have to find that happy medium.
I DO like the idea of having price changes over time. For instance, at mid era, medium drones should be pretty pricey, but affordable. Instead of then seeing fast drones at double that price when they come out, you could edit the prices so fast ones now cost what medium ones did, and the mediums become half as expensive. This way, it's the same cost per drone to keep a ship stocked in any given era, or you get rewarded with savings by using lesser drones.
Similarly, repairs and spares could be made less expensive at the beginning of a campaign, to help players bear the burden of weak ships, and then become pricier as the campaign advances, reflecting the difficulty in keeping up with the demand for new ship parts and the price of training crew -- after all, if you come home wounded, chances are you lost crew, who have to be replaced.
Marines can probably be made reasonable again as long as you take out of the shipyard (class as special) the over-the-top commando tugs and what have you that load near a hundred or even more boarding parties.
Mines I don't think need to be all that expensive -- they are not usually a balance issue as far as I know.