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.

Systems failing on damaged ships doesn't sound like a bad idea but I REALLY hope they never go with "hard point" based capital combat the way Star Wars:  Empire at War did.  If a specialized unit could try and perform surgical strikes or you could give a general order to try and take out the engine to try and capture of ship or even say a cricial hit system that could disable system wouldn't be bad but but the way EoW forced (pun intended) you to targer hard point, after hard point, after hard point was really obnoxious and in my mind really defeated the purpose of the system and undermined the whole concept of trying to disable a specific system surgically rather then going the much easier road of just trying to destroy the enemy ship buy blasting it till its super structure buckles.  Just my opinion but I really hope they don't follow the EoW road particularly since you frequently have to look away from a battle to manager another part of your empire in real time.

@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.

I would like to see use of a sphere around the planets instead of main fighting to be more flat.  Every once and awhile my ships will fly over the planet but normally they go around.  it would make placement of sturctures more than just the horizontal

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."

Hegemonia hmmm?   I'll have to look into that.  Thanks.

One additional note.  I think we would need better fleet movement AI for the hard point system.  In addition to the problem with ships moving irrationally when going to an objective the AI would have to be smart enough to turn ships while in combat to shield damaged or weak sections from enemy fire.  Currently they only seem to pivot to get the most weapons on a target and the AI would have to know when to arrange itself offensively to bring the most weapons against an enemy and when to move defensively to keep its weak points protected since we really don't have a manual command to tell a ship how to arrange itself in relation to an object once it is at the destination we ordered it to.

 I would LOVE to see another race completely space based, ie it doesn't use planets for its economy in a traditional sense, so it would use economy ships to raid enemy planets, asteroids etc, ships that construct their production facilities in gravity wells etc but as mobile and nomadic as possible.

 Not the best multiplayer race but gosh this would be fun to play single player!

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.

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@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)

Dooling at the possiblilities for this game....in awe

Imperial Capitol Ship.

(Yes it is EVE but just ideas compared to other ships

Caldari Mother ShipWyvern

http://www.eve-wiki.net/index.php?title=Wyvern

Cldari Titan Leviathan

http://www.eve-wiki.net/index.php?title=Leviathan

I wish the Flagship did more then gain the senior mark....

Imagine the fear when this ships rolls into a gravity well.  The only way to make it fair would be to make it crawl.    Hmmm and take crystal or create a new column and use ti to jump systems.  New mining roids, which the big ships use for fuel and if you run out they dont jump.  In addition to antimatter