I guess it could be argued that not all ships need it, but a good question to ask is how many people don't choose Loadout Design 3 in their games?
I'm pretty dependent on that extra OP, so while not having it is technically not a reduction in OP, it does seem a bit like it in practice. However I don't know whether this is true for other players (you don't necessarily pick it all the time as you mentioned), perhaps I'm in the minority with Intrinsic_parity in thinking that it is super important.
With story points I'm almost certain to be able to actually squeeze more OP into a ship with the hull mods, but rather than being a specialization, I'm thinking about integrating the most expensive hull-mods first to free up the OP lost with the absence of LD3. I guess it would feel better to me if integrating hull-mods with story points was an upgrade rather than being a requirement of getting that additional OP I count on in 0.9.1a.
I admit though that once I see the new mechanics in action, perhaps I will change my mind, and I want to emphasize that I'm genuinely excited about the new skill system overhaul; it just seems very much more interesting than the current system. I'm just greedy when it comes to ship customization!
A possible compromise would be to create a hull-mod that gives that 10% additional OP of "Loadout Design 3". Perhaps make it logistics based (was the limit on those 2 right?), though that may mean buffing other logistics hull-mods so that the OP reduction hull-mod doesn't become the default choice.
Building on this idea, how about offering several unique hull-mods only available with story points?, some random examples:
"Lightweight Weapon Mounts"
- OP cost reduction per size class of weapon (Small: -1 OP, Medium: -2 OP, Large: -3 OP)
"Waste Flux Re-Routing" <-- I struggled for a name here....
- +50% to Energy Weapon damage at high flux levels
"Hull Repair Droids"
- +0.5% Hull integrity restored each second up to 50% hull (maybe requires 5 seconds of not receiving enemy fire to activate).
Ignoring my randomly chosen bonuses, these unique hull-mods could be more expensive in story points, and be of a limited amount (eg 5/10 per game, but refundable) so that they don't end up replacing all the standard hull-mods as the de-facto choice. You could even make these special hull-mods into something that you need to acquire through salvage rather than be given immediately.