I haven't played much with missile ships, what is your Gryphon fleet build that can autopilot through Ordos fleets?
Squall, double harpoon pod, breaches, all in one linked group. Officer with TA, Missile Spec (elite) and SysExp. You will also put a converted hangar of your choice, but it doesn't really even matter, missiles obliterate everything from 2500 range anyway.
The issue I have with the "specific challenges require specific strategies" argument is that it simply doesn't apply to Starsector. You don't need different fleet comps to beat different challenges. Any fleet that dumpsters ordos also dumpsters any human faction fleet (the opposite isn't true), so the only strategies worth using are the ones that work against ordos. Anything else is "fake content".
Don't forget the new player experience, too. It doesn't feel good to find a nice fleet comp, s-mod your ships, fine tune officers... and then have to throw it all into trash because it doesn't work against remnants. Human fleets up to this point were all doable, the game never told the player he was "doing it wrong".
Cerberi with vulcans only are obviously not what I meant. Here the
ship loadout is suboptimal, this should indeed be punished.
Ships themselves being bad is the problem.