Sure, 'git gud' might be one aspect to it. I've only played 10-15 hours, and I'm still mostly rocking the hammerhead I started with. I recently switched over it's loadout to 2x Heavy Autocannons and 2x Anhillator Rocket Launchers to try to mix anti-shield and anti-armor. I figured I'd bust the shields and rough up the armor, then duck back out and let some of my frigates pound on them while I burned flux. With 8k flux capacity and 420 flex dissipation I figured it might work. But my perception is that the AI is smart enough to let the AC shells through and shield-tank the rockets. The last few times I've tried in sims and against relatively even battles I tend to get overloaded when I dive in, before I can drop back to bleed of flux. At this point in gameplay (still probably early game) it feels like the AI can stun-lock me fairly easily (via overload or by forcing me to vent flux) while it seems nearly impossible for me to the same. I don't expect to punch above my weight class, but an even destroyer-on-destroyer fight I'd think would be a bit more balanced then it feels like it has been.
Gave this kind of loadout a try just now to see how it feels! Fought a simulation Hammerhead and Enforcer (the first one of each). Seems like the AI will shield-tank the Heavy ACs until it's a bit over half flux, at which point it'll generally start armor-tanking. Ideally, it'd really armor-tank the ACs earlier; I'm also not seeing much shield-flickering going on - it pretty much just turns them off, and occasionally toggles them on to block the Annihilators. But, that's exactly what I'd be doing it its shoes; in a fight like that, that's what you want to keep an eye on - blocking bursty HE with your shields.
I'll say, though, this loadout is a bit tricky to fly. You have to engage the ammo feeder at the right time, keep facing the enemy, and then hit a moving target with Annihilators, which is not the easiest thing in the world. Plus, when facing destroyers, it's just *really* lacking in finishing power.
The Annihilators just don't cut it vs armor - I think this may be at the crux of what you're experiencing. This loadout has way better kinetic damage than it does HE, so pretty much no matter what, if it's facing decent armor, it'll end up hitting it a lot with ACs, which is inefficient and will lose you the flux war. The Annihilators are - in addition to being hard to hit with and a bit under-powered as a main source of HE - also bursty, making them easier to block with shields.
What I've observed flying it is I start winning the flux war very handily early on, but just can't capitalize after that. It seems like it could be a good support loadout, but it'd probably be better off mixing in more HE somehow. Either one Heavy Mortar, or two and kinetics in the two small forward-facing turrets, plus Sabots - something like that. Or even some Light Assault Guns in the small turrets, while keeping the Heavy ACs. It's a decent shield-cracker as is, just has no good follow-through.
I'm certainly willing to entertain that my biases are limiting my tactical vision, but when I saw the game had modding support I figured I'd jump in the deep end and see what I could do. I was frustrated enough that I considered shelving the game, but given how enthralling it is in general I thought a shot at tweaking this annoyance was worth it.
Fair enough, and I very much respect the impulse to mod things you don't like!