In keeping with the space-combat focus of Sins: :

Directional Physical Armor: Armor plate strength varies between bow plate / stern plate / flanks / belly / top deck.  This creates an incentive for flanking and envelopment tactics, or the like - or the developed of guided missile techs. An implication is that it creates different tactics for races or ships which use primarily physical armor vs. those who rely heavily on shields.  Shields, barring funky shield mitigation roles, might reasonably be omnidirectional as it were - whereas plate armor is protects a physical quarter (bow, flanks, stern, top deck, belly), and therefore does not distribute to other areas.  The emergent effect I see is that ships relying heavily on shields might be more resistant to focused attack from a given direction (since all shield energy is available to mitigate it), but heavily armored ships are conversely more resistent to being "swarmed", since attacks to one quarter do not affect the armor elsewhere.  This would, in turn, imply that a physically armored TEC ship is better at standing in the fray, but might succumb when trying to run, presenting its lighter stern plate to attack.  A shields-heavy Advent ship might be better at a fast hit (soaking frontal damage) and run (soaking stern damage with l chance of having the drives disabled), yet its shields can go down quickly when swarmed.

Hit Locations / Structures: With hit locations & ship structures mapped to given hit locations, combat again can become more complex.  For instance, a stern hit is more likely to disable drives than a hit elsewhere.  This also raises the the notion of tradeoffs between weapons that are mobile (turrets), hence less armored, vs. fixed inboard weapons, which are protected by the main ship plating.  This, in turn, means that weapons with greater traverse aren't necessarily better: they are usually more vulnerable.  Logical ship structures might include Drives (stern (?)), Powerplant/Reactor (ship core), Frame (all locations), Heat Sinks, Magazines, Weaponry, Special Abilities, Fire Control, and Commo.  Some of those features, however, would get into some slightly more complex rules.

Anyways, this is perhaps not truly reflective of Sins mechanics, and might overtax some systems anyway.  Obviously, this might also make life hard for the AI programmer; perhaps this an approach best suited to human vs. human.

@tymestar and LaFreeze
Well, if you've ever played hegemonia (or haegemonia) - Legions of Iron or its sequel you would know how it is done right! (And it had things right in so many ways, just not in respect to diplomacy, trading or modding...) You could assign ships targetting priorities (hull, engines, weapons) so the small ships would target the weapons while the big guns targetted the hull, or you could stop ships by targetting the engines.

I would wish to have the battlesystem diversity and the sabotage options from hegemonia and the trading and diplomacy options from Civ4

Too much to ask for.

Tobiwahn, thanks for the heads-up on Hegemonia.  I've not played it, but it sounds worth checking out.

LaFreeze: Good point.  A hit location / directional armor system not fully thought out is worse than no such system.  In such a broad game as Sins, player attention is a scarce commodity: if units don't have reasonable default or toggle-able targeting scripts, "battle fighting" could turn into "painful battle micromanagement."

Restlessmind's suggestion brings up the same interesting gameplay implication that I think hit locations & ship substructure does: the elimination of focus-fire as the be all / end all of combat.  With incremental ship disability, distributed fire gets a new lease on life.

@Valaska
You might try out the TriPirate mod

https://forums.sinsofasolarempire.com/369301

of EvilTesla-RG, I think he had such a thing in mind with that mod (not completely, but almost IIRC)