Yep, checked weapon stats and tested in-game (tier 4 missiles against tier 1 PD, no less), there's still basically no reason to use missiles in vanilla. I bumped up their evasion and speed slightly (increasing with tier), massively increased their range (the same), and changed PD damage & missile health such that top-tier PD won't one-shot top-tier torpedoes or missiles (or Large tier 4 missiles), and only has about a 50% chance of one-shotting a missile of roughly equivalent tier. I also bumped PD accuracy down a bit so that it scales from 50% to 60%.
Basically this way you still have the distinct advantages of the different other weapon types, but missiles now have their own advantage of standoff range (longer for larger missiles, though smaller missiles also have better speed and evasion). It also means that PD isn't a perfect hard counter--generally with this setup you should need slightly more than 2x as many PD turrets as the enemy has missile launchers in order to shoot down everything, whereas in vanilla you could almost do it with fewer PD turrets than there were launchers.
However, to remove the possibility of late-game cheese with corvette missileboats kiting forever, I gave the energy lances, kinetic artillery, and large mass accelerators (basically all the yuge cap-ship weapons) much longer ranges and slightly improved shield damage/pen stats (varying) so that they could outrange all small missiles and most (in some cases all) medium missiles. Of course large missile still retain a (slight) range advantage, and all missiles have lower cooldowns than those big guns (and also better accuracy), meaning that there shouldn't be a point where battleship snipers can just pew pew missileboats with impunity. Torps are mostly fine where they are now, but I gave them a slight tier-scaling speed increase.
That, and I gave the autocannons a slight tier-scaling cooldown buff. They're supposed to be short-ranged chainsaws, they should act like it. Also bumped strike craft attack and recall ranges waaaay out, to something like 2.5x the maximum range of any other weapon, which is still absurdly short for carrier-launched fighters but with the game's scale the way it is...
Tentatively, it looks like they might have unfucked combat behavior for real, so I didn't touch that.