I've no particular problems with missiles as they are now for player use - there are some that I simply won't use due to low ammo count (specifically the harpoon pod and the sabot pod - for a medium missile slot I'd much rather use LRMs, Annihilators, or pulse bombs), but overall they work fairly well.
The problem that I see is that the AI doesn't know what to do with sabots - it treats them the same way it treats harpoons vs. armor, firing sabots off whenever it thinks it's got a good shot at hitting shields. Which would be okay if they did super-hard-flux that couldn't be dissipated... but they don't. Limited ammo in your armor-cracking weapons is fine, since your opponent has limited armor. Limited ammo in shield-breakers, though, doesn't work as well. Again, the player can manage that limit and get good use out of sabots, only spending them when it'll give you a chance to deal permanent damage. But the AI can't do that, and it makes AI ships with sabots rather weaker than they should be.
Now, maybe this is a place where the AI can be fine-tuned; we can now mod in per-weapon firing AIs, and attaching such to the sabot launchers might resolve this. But AI is hard; making the missiles regenerate is much easier.
