I've modded some changes - actually most of if addresses the stuff mentioned here.
First of all, Corvettes are very versatile because of their possible loadouts, especially later in the game when equipped with Torpedoes they can shred even Battleships easily. So I removed the Missile section for Corvettes and left there only the 3xS and 1xPD+2xS sections.
Then I gave to Destroyers Missile sections so that they can serve as the first real rocket carriers.
Making loadouts like these possible:
But ofcourse you can have the Stern section 2xS to have a Missile and 4xS in total which works nice against Corvettes too, due to the high tracking of Missiles. Corvettes can have PD sections too so they are not completely screwed against Destroyers like these but the PD counters the rocket slot and the Destroyer is still left with 4xS guns while a Corvette at this point has 2xS guns.
Anyway, I've also reworked the Strikecraft. There are Interceptors and Bombers again. Interceptors have high tracking and their targetting priorities are highest at smallest ship and go down to the biggest ships - so they go after Corvettes first, then Destroyers, Cruisers, etc. while Bombers have low tracking but their targetting priorities go the other way - start at big ships and stations and go down to Corvettes. At the same time Cruisers got one more possible Hangar section at the back so Cruisers can carry two hangars.
The fact that interceptors go after smaller ships first makes it important to keep some PD corvettes and Destroyers in fleets too, so if opponent uses Hangar defense stations or later Cruisers with Stricraft, Destroyers like these are also quite useful.
Also later on when you get your hands on bigger ships, it is not a bad idea to design Destroyers with Missiles and lots of PD to defend your Cruisers and BBs from Bomber Strikecraft in case the opponent builds them.
I'm not sayin it is perfect. I'm still tuning the settings (especially the Strikecrafts and PD) but seems to me it works better than what vanilla game currently has.