I do not currently know enough about starsector AI modding to achieve this, as it would require AI hooks, however, here's an idea I had about a slight rebalance of reloadable missiles.
Instead of having missiles reload all the time (something I personally find slightly better than not reloading at all) there should be a hotkey to press, perhaps V twice, that would set a ship reloading ammunition.
This would only happen at 0 flux, and would be disabled if the ship fired any weapons or attempted to move. A few seconds of uninterrupted reloading would be needed per reload cycle, perhaps 3 seconds or so, and this would reload 10% of all reloadable weaponry. As such, to reload a 3-shot rack or a single-fire torpedo would take 30 seconds of sitting there doing nothing, and would not often be allowed by the AI or desirable... but you COULD sometimes get the time (10 seconds) to reload just one missile.
It becomes much more plausible with a 50 shot pod or something, where even a single reload cycle gets you a few missiles to work with.
If further cost is necessary (though I don't especially think it is) then you could impose a slight CR cost for doing this.
Might have a crack at the mechanical implementation of it later, though it'll be strictly player-only for now. Opinions? I'm leaving this in Modding rather than Suggestions because I don't think it's a viable suggestion in vanilla gameplay, it's just too fiddly - but I do like the idea overall, and think it would fit well as a mod.