I would prefer Neural Link not to use hullmods, but I cannot think of a better way to mark ships. Neural Link as-is should not even be a skill, let alone capstone, just gated by hullmods. (Just use Neural Integration for all ships for a non-skill version of Neural Link.) The OP tax on two ships (including the flagship) hurts too much. Same thing about any OP cost is too much for Converted Fighter Bay on Tempest or Venture, who do not have OP to spare. (It is silly on Tempest, pay OP to weaken combat power? No thanks! Then again, NPC Tempest wastes the drones, so maybe not. Still not worth the OP tax.)
As for Expanded Deck Crew, it does not do enough for its cost. Previously, the bonuses were two-and-a-half times more than it is now, and that was too good. Now, the OP cost (which has not changed) is too high for the measly bonuses (compared to the carrier skills) the hullmod gives.