Here's a random one kinda stolen from Reddit.
Picking certain skills unlocks hullmods more or less associated with the skill. For example picking the Flux Regulation skill automatically unlocks the Resistant Flux Conduits hullmod. This is generally speaking of absolutely minimal use since most hullmods are available on the open/black market for pennies and the really rare/good ones like ITU cannot be unlocked by skills in the first place.
But now that hullmods are going to have bonuses(or penalties) when S-modded, why not combine the two systems? For example picking Flux Regulation unlocks RFC, but also means that RFC will provide the S-mod bonus even when not built in. In case of hullmods with penalties, the penalty can be made smaller.
There are some balance concerns with this idea though, for example if the hullmod bonus applied to every ship it would make combat builds even stronger(i.e. you get Field Modulation for your flagship -> all ships in your fleet with Hardened Shields get a bonus) so it probably would have to be limited to hullmods on the flagship only.
