@ Wapno
Flux positive firing of weapons only occurs when a.) you have SO's bonuses (and thereby reduce your longevity and range) or b.) when you max vents and use relatively weak weapons. Most of the ships in the game, especially the low-tech ones, are extremely flux starved. You can't be flux positive on an Enforcer without going almost all small mounts or PD. The point being, the only way to stay flux positive is to gimp yourself in some way, which is the same argument being made for limited-fire missiles. "High damage, all the time" doesn't exist without a trade-off and not utilizing missile mounts to save OP is typically not enough. I'd love to see some of the non-SO builds you're using where you can achieve this. SO is an exception to the rule and has its own strengths and weaknesses. It can't be used as a "typical" build.
Missiles allow for a ship to operate outside of its typical role. Or to put it another way, missiles have always been supplementary. They are not primary damage dealers nor are they intended to be so. The only ship in the game where this is the case is the Gryphon and it has a ship system to regenerate missiles. The "friggin Kite" can only hurt a Dominator with missiles. No amount of "proper vents, guns, and hullmods" will help a Kite defeat anything larger than itself. It takes the two missile slots to actually do something. Yes, the Kite is an extreme example but as I look across the board, very few ships have a ton of missile slots and most are used to supplement or compliment your primary loudout.
As I look from a "macro perspective," I don't see this as a zero-sum game. You can have hard-hitting, tough ships that also can nuke a dangerous target if the opportunity presents itself. I don't see why this has to be all-or-none. I have a very effective SO Hammerhead build that is flux positive and then I mount two Reapers up front. I could have saved 4 OP but for what? What can 4 OP get me that is better than insta-killing a highly-dangerous and tough Cruiser, even if it's only once? Had I omitted the missiles, I can whittle down the cruiser but in the mean time, it's still firing big guns at my fleet. I see eliminating the most dangerous targets as a much stronger damage-mitigating tool than adding a hull mod. But, that's the old argument of "the best defense is a good offense."
But that's also why I oppose regenerating ammo because that Hammerhead, if given another minute or so to reload, could do that again, and again, and again...for 4 OP and 0-flux. You'd have to rework the entire missile system to account for regenerating ammo.
Finally, what kind of fleet actions are we talking about here? Early game, end-game, or...? If my early Wolf can use missiles to take out a Destroyer, that's absolutely a win, even if I can't do it again. The Destroyer was probably the biggest threat anyway. Taking out key ships is what causes momentum to shift or again, acts as a force multiplier for me. If I can't exploit temporary weaknesses with high burst damage, the bigger ship wins (with bigger guns, more vents, etc.), all other things being equal.
@Megas
Regenerating missiles are not the same as carriers with fighters (with/without missiles). Carriers have their downsides, namely being relatively weak in and of themselves and having a mechanic that slows down the regeneration over time. I doubt there would be any slowdown effect to the missile regeneration on a combat ship. It would likely be a fixed timer. Spamming bombers from carriers eventually gets the carrier into trouble and unlike combat ships, a carrier's "weapons" can be eliminated and thus, increase the time of regeneration.
For as strong as carriers are in this iteration, they still have factors that work against them. Regenerating missiles would have no drawback beyond reload time which, if you don't re-work the OP costs of missiles, would have to be high enough that balance isn't completely thrown out of whack. I hope no one is suggesting that Harpoons/Sabots have anything less than 1 missile/minute reload times. For a typical frigate, that raises one 3 OP rack from 3 shots to 6-7, assuming you use them early before your CR begins to diminish.
Now, if implemented, that means your average Wolf is going to be able to spit out 12-14 Harpoons/Sabots over its CR duration. That's twice as many missiles. It would be higher as the ship size and CR limits increase. The question I ask myself is: do I want 2-3x as many missiles flying around? Or perhaps more importantly, would regenerating missiles create a situation where I no longer value the limited supply (i.e. use them with abandon)? I'm a big fan of opportunity cost so using a missile now means I can't use one later. If I could count on regeneration, that decision-making is basically eliminated. I'd rather have the AI use them more intelligently rather that use more of them, to be honest.
As it relates to carriers, there's nothing I can do as a player from keeping that Wolf from firing 12+ missiles but I can slow down the rate that a carrier's fighters can be replenished. They are comparable but not indistinguishable. If every combat ship had twice as many missiles at their disposal over the course of the battle (even if it slows to a trickle after the initial volley), I can't do anything about that from a mitigation perspective besides slap on more PD or hope I can disable a missile mount via damage or EMP. The question I have to ask myself is: are twice as many missiles in the game good or bad? (And I would argue this needs to be taken on a missile-by-missile level. I agree with Megas on MIRVs, for example.)
Again, if missiles are intended to be supplementary (which I think is obvious from their current use and how their mounts are placed on hulls), does regenerating ammo enhance or sabotage this role? It would make using them less of a gamble but in essence, you've just created very slow reload weapons. I'm still a fan of high-risk/high-reward weapons but I admit, the AI needs to use them more intelligently.