Alex, what if you made it so enemy fleets decide to make a last stand if you're faster than them and have harried their retreat once or more? Later on, you could add campaign fleet AI that would weigh their chances of making it to a friendly fleet or station before being harried to death.
By the way, about supply costs, for present game balance wouldn't it be easier to reduce the price of supplies to close to what it was before, but reduce the amount of money provided by defeated fleets? You could also make supplies have a poor resale value. Considering that supplies are supposed to be assembled (either from a store or a wreck) for the needs of your fleet specifically, selling off a large quantity of them would be the interstellar equivalent of a yard sale. It seems like one of those would be easier than redoing the prices for everything else, which are about where they need to be relative to each other. It's all about relativity.
@Debido I actually like the way missiles work in this game. Granted, it in no way resembles how any real missile would function, but they are an effective and unique weapon on the battlefield. The presence of missiles, more than being an immediate threat, serves to heighten the tension of a battle: they sap your focus; they limit your mobility; they eat up flux with point defenses and shields; they distract you from destroying your enemies; and if you should, for even a moment, forget their presence, neglect your defenses, they will destroy you. A Salamander in the engines can send you pinwheeling through a cloud of missiles you were dancing around a moment ago. A Sabot carelessly taken on the shields can overload your ship instantly, leaving you defenseless and unarmed while surrounded by enemies. And torpedoes, oh god, just... don't get hit by those.
I do like the idea of tying CR loss directly to combat, at least partially. You could still keep the current dynamics. Make CR deployment cost a fraction of what it does now (small reduction for capital ships, bigger reduction for frigates) and introduce in-combat CR drains: weapon use, damage (shield, hull, or armour), engine use. These drains could be weighted more heavily for smaller ships, simulating easy to deploy, low-endurance craft versus more logistically involved, but more independent, ships. With all these fancy new system failure mechanics it seems a waste to only use them in scenarios brought about by poor management.
