The only problem with missile regeneration is you need full reload between rounds... which I have no problem with.
And a common misconception is that missiles need some kind of replenishing. If you get expanded missile racks, a lot of medium and large missiles ammo can easily outlast a fight duration. For instance, 1200 locusts take around 270 seconds just to finish firing if you fired non-stop, every single time it is off-cd. A medium reaper pod with exapnded missile racks would still take 150 seconds to run out of ammo if you fired non-stop every time its off CD. The only medium/large missile that I found to actually be limited by ammo are sabots, and even then its rarely the case with judicious use in fights.
Locusts with expanded missile racks is literally the best case scenario. Even that runs out during the ten capital spam that is common at endgame fights, and they do not reload between rounds. At least that will last for most of the fight. Anything else not named Salamander will run dry too quickly.
I have abandoned Annihilator Pods on Onslaught due to them running out too quickly. I now put either Typhoon Reapers or Salamander Pods (or even leave them empty) on Onslaught. Occasionally, I put Swarmers with Expanded Missile Racks for anti-frigate at the rear, but even those do not last significantly longer than Annihilator Pods.
As for missiles...
Harpoons are spent as soon as the first target is vulnerable. Okay early in the game when there are fewer targets, but by endgame, they might as well not be there. They are very vulnerable to PD. Probably needs Missile Specialization to make them decent.
Sabot are great under player use, but not so much under AI use. AI chucks few here and there, or unloads when it panics. Either way, AI uses them sub-optimally.
Hammers are cheap, common, and AI is decent with them. They do not last long, but at least you get what you pay for. Wished there was a medium Hammer pod. (Hammer Barrage would be fine if it either had more ammo or costs only 16 OP, ammo runs out too quickly).
Atropos is a tad too weak for its price, and too similar to Harpoons. Hard to use at times due to narrow range band. Too close and they bounce. Too far, they flame out and bounce. Would like to see 1200 damage. Stupid Dagger spam ruining it for normal ships (much like Mora ruining Damper Field for frigates during 0.8.x).
Swarmers are decent anti-small ship. Run out a bit too quickly, though not as fast as Harpoons.
Annihilators are good mostly as a defensive screen and occasional finisher. They tend to be my missile of choice for smaller ships. Still runs out somewhat quickly in big fights.
Reapers have their uses. I use them mostly to cheese kills with Afflictor (now that Harbinger cannot do that anymore). Not straight forward to use since they are slow and fragile without skills. AI is conservative with them, and may not run out after a minute of fighting. Large Reapers are too expensive, take too long to reload, and too few ships can use it effectively.
Salamanders are basically an unlimited homing stun gun that can distract. Occasionally useful. Sometimes mounted instead of nothing if I need something to last a whole endgame fight.
Pilums stink bad enough that critical mass is probably impossible without maximum map size and maybe ten officers with Missile Specialization. I try Pilum spam with missile ships (without skills), and while they blot the screen and look intimidating, they still mostly fail. Best case, they kill one ship before ships run out and wait to regenerate more. Usually, nearly all Pilums get shot down, blocked, or flame out. I had better results with most other missiles. I think Pilums are bad enough that no weapon is better than Pilums, much like Thumper in earlier releases.
Proximity charges are too slow and burn through ammo fast. It is like the bomb bay in a missile slot, and it costs 12 OP. Too hard to use for too little payoff. Another no-weapon-is-better-than-this weapon. Flash wings use them to good effect, but they do not have pesky ammo limits.
Locusts are great. Excellent tracking and lasts long (but not long enough without Expanded Missile Racks). Murders small ships easily. Even big ships take big damage if armor is stripped. Even better, they are cheaper than other large missiles.
Squalls stink. They track poorly and run out of ammo too quickly. Worth too much at 20 OP.
MIRVs are too expensive. They need more than 25 OP to do well. They need ECCM and Missile Specialization for payload to converge properly. Probably needs Expanded Missile Racks to last long enough too. If player can get all of that, MIRVs are probably good. In any case, AI does not conserve MIRVs at all, and fires them at every opportunity. Without all of the support mods and skills, MIRVs are just something to use if they are available but Locusts are not.