Firstly, I think that as the idea of fighters being weapons holds nicely I thought of something else: how to encourage people to use carriers as flagships? If they can't be combat-oriented ship that means they would have to have some other mechanic to be useful. That leaves us commanding, which is, as of now, less interesting option, since you can give 3 to 13 orders in a battle, the less you care about it the less you invest there the less you can. Besides enhancing leadership tree (which is another question entirely) you can make it more viable. For example, by making orders free under specific conditions, like having some high-strength battle communicators hullmod mounted on carriers and the ship on receiving end being in certain distance to a flagship. That would give 3 things: make being commanding commander more viable, make fighters act like a weapons (because weapons have a feature that basically is "they strike where you point") AND it would give an edge for certain ships (I'm thinking of Condor, Venture, Conquest, Odyssey). I think it would be best for such comms to be either built-in or as an 5/10 Advanced Tactics hullmod. For even more restrictions, make it work like a weapon, limiting it to "free ordering" to one ship and with some cooldown when linking with another ship.
Secondly, give some indication of incoming
warp hyperspace storm so a player can manipulate fleets to trap them in there.
As fas as I know, they have no "foreshadowing", they just happen.
Last thing is too complicated for Alex's taste, probably, but I'll post it anyway: instead of (D) variants give ships a condition stat that would be restored by metal (for all ships), heavy machinery (Core, Expansion) and rare metals (only Expansion) and past certain threshold(s) down the line a ship would get those flaw hullmods. Though the more I think about it, the worse it sounds (most importantly, it would be hard to balance so as not to make it either "too important", "barely noticable" and "CR #2").
