I like both the regen-to-one-salvo mechanic and the flux cost while regenerating to that one salvo ideas, personally.
I'd also support having the rocket style pods regen in chunks with a long regen time, to get a break between firing periods as someone suggested.
These ideas would keep missiles somewhat different from the other weapons, maintain their limited high-alpha low flux role in battle, and still preserve missile ships as not as useful after they've fired all their missiles, because now they have flux and can't even fly as fast until they've regenerated the next (batch of) missiles... but it would fix them being entirely USELESS after they're out, and it would make adding missiles to ships feel so much less a waste of OP if you're planning to get into any larger battles.
Even if you don't want to do this for the main game Alex, please would you check/add the ability for us to mod in regenerate-to-X ammo, and/or flux while reloading? I'm aware that, if you don't go with it, it's time away from full game features, but it would open up lots of subsequent ammo based possibilities for all sorts of mod weapons (many of the spinal giant cannons would benefit from less flux cost but then flux-while-reload, for example) and I'd love it for pretty much all missiles.
Without those features, I'll probably still add a slow regen to all medium or larger missile mounts. I think I did once for a previous version, forget which now. In fact, Serenitis, if you would consider posting your mod somewhere I'd appreciate that, I'd certainly use it, even though I'll probably keep racks as zero-reload without the ability to limit them to 1 missile, as otherwise they can build up another alphastrike and are not costed to be able to do that more than once.
Edit: Before someone asks... yes, I absolutely do selfishly want these things at the expense of other stuff, like a sooner release. And you should too, they're useful options with loads of potential. You'll thank me for it laaaateeerrrr... *is dragged off and devoured by the update-hungry masses*