@Factions: I think we should take the persona-centered route, but try to select "commanders" for the factions that are quite different in personality and tactics used. so, like for example (example, not necessarily suggestion) the Schwarz Lanzenreiter (Black Lancers) as a elite offensive subfaction of the Galactic Reich with less focus on building and defense, and more ship-based tactics. so they are pwnage in ship to ship fight, but somewhat weak when it comes to multiple front battles and using your ressources efficiently (higher costs, longer build times, whatever), maybe even to the point of having abilities that disable enemies / cause some of them to flee (which is an interesting thought, is it possible to trigger the retreat function and make it un-overridable for a time?) because the Lancers are SO evil and badass that every pilot who knows them cowers in fear knowing they are coming. or something like that.
Another possible example for a quite similar offensive faction on FPA side could be the Rosenritter, even though i know they hadn't that big of a role in ship combat, but you could always make them specialised in invasions, with worse ships than the others but cloaking abilities (disguise as civilians) and better (maybe faster) invasion abilities, could try to board other ships and overtake or disable them, or something.
again, i know these examples aren't really perfect, but i guess you at least know what direction im aiming at ^^
@Mechanics part 1 - Infrastructure: I really like the notion of a big badass drydock/factory complex, one thing i dislike a bit in sins is that ship factories are not really vital, they are cheap, and they are built in no time, so if your enemy even bothers to destroy one or three of them, you won't care too much. As it was already somewhat decided that ship building should be slower and more expensive in LoGH, it would make sense to apply these restrictions to the factory as well, or more like especially to the factories. so, they are big, they are hella expensive, they are nothing you want to stick around on your frontline just in case someone decides to pay a visit while you're not at home, because you don't want to be cut off from production for how long it may take to build a new one. On that note, i think they also should eat up considerable amounts of tactical points, to the point where you can't just build one at any planet you come across, but you have to have a few dedicated docking planets, where your production facilities are placed, and these are the vital points of your military. Another passing thought on that, it could be made that you can only build big factories at ressource rich asteroids or something comparable, because of the ressource intake necessary to build freakin huge ships. would be a bit limiting if applied to every factory, but maybe split frigate and cruiser/carrier factories? if possible even limit the repair capability of factories to the kind of ship they can build/aka the kind that can fit inside to be repaired, but thats just a vague idea.
@Mechanics part 2 - Civilians: One thing that crossed my mind a few days ago, was civilians. A big thing in LoGH is the interactions with the civilian population, and in turn in some cases disguising yourself as civilians (or enemies for all that matters, iserlohn anyone?). so, would it be possible to make a civilian faction which is always there, AI controlled which for the most part just trades and is simply there? this would open up many possibilities in conjunction with "Public Relations" of some sort, you can't just fly around and harass the civilian population, or blow their ships and stuff up. And it would make sense that most non-military (orbital) structures are civilian owned and can just be aquisited by you (the military) for temporary use (like neutral mining platforms in SINS), on the other hand, the people aren't happy if you go around taking all their stuff, so maybe if you overdo it and harass them a bit too much, you get revolts and allegiance drops on your planets (as seen on heinessen in LoGH for example). Similarly you could have abilities that disguise you as civilians (IF technically possible), and the enemy may somehow notice that maybe this civilian trade ship is a bit strange, steering clearly for his planet and all, but does he want to just blow it up just in case? if it really IS a civilian ship, that would't exactly raise the public opinion of him. if he decides not to, it may well be a disguised assault force, inciting revolts or even taking over his planet (see it as liberating the populace from the oppressors by assassinating most loyalists and military leaders, if its strange to imagine that one ship can take control of a whole planet). Possibly the Civilian faction could be merged with phezzan, so that if you piss them off enough, you can't use the black market anymore, or something like that. people, after all, react a bit allergic to tyrants in most cases. on the other hand, civilian traders/freighters could be hijacked/aqcuisited for emergency frontline support or the bit of money you need to turn the tides, at a cost, that cost being diplomatic repercussions. for this whole thing to work, it had to be possible to set a faction as fixed neutral / ceasefire the whole time, with some things happening if your friendliness meter drops too much, but the whole thing stabilizing after a while and going up again, so maybe a base default value of 50% and a ceasefire, to which it returns automatically slowly, and drops/gains by doing specific things (gains by giving them money, liberating worlds but leaving them neutral = in civilian control, etc., drops by attacking civilians, acquisiting their stuff, etc.)
This all is a bit complex and i don't know how possible it is to implement without maprelated scripting and stuff, but i think it would be a really cool addition. feel free to discuss and make corrections if something is absolutely stupid in your eyes.
@Mechanics part 3 - Supply routes: One thing i almost forgot: i had an idea how supply to fleets could be done: if this is possible, you could create another variable value for ships, like antimatter but just call it, i dont know, simply 'supply' for all that matters, which drains slowly by itself, and is restored by supply ships (which could have an area of effect supply restore ability, don't know if its possible to fit automated ships like trade ships with abilities, but should be i think), OR you can make it that the supply value drains if no supply ships are around, but refills if one or more supply ships are in the same grav well, or in the vincinity of the ships. and for the necessity of keeping supply up, just make an automatic debuff gimping all ship values if supply is low, or even zero. so no ships blowing just up if they are out of food (which would be funny but stupid), but reduced functionality because the crews are really really hungry and can't work properly without enough food (and for simplicities sake, lets just say supply zero isn't really NO food in the sense of completely nothing left, but its down to extremely limited emergency rations for everyone, which isn't that morale-lifting normally)
One synergy with my proposed civilian system would be that you can restock supplies by pillaging civilians (as often seen in LoGH), but that would cost you a lot of diplomatic points with them. on the other hand, you could give planets the same supply value, and be rewarded points for sharing your supplies with planets who are low on them (because of enemy actions maybe), planets could refill their (takeable) supplies automatically but very slowly, and you would be rewarded for everything you give them if they are below half maximum or so. just an idea, but i think it would fit in nicely if tweaked a bit for usability.
@Mechanics - Addendum: One thing that would play together nicely with most of the above, would be a clear difference between specific planets. like, one planet type which is prosperous and rich, has a LOT of supply and stuff, and much money to milk out of them if you take it under military control, another planet type which is rich in natural ressources and can support heavy shipyards and stuff, as opposed to poorer worlds which aren't that good but can be used to redeem you for your militaristic actions by placating the civilians if you give them food and freedom. phezzan as the hub of economy which could seriously affect everyone on the map if taken (embargos and stuff maybe) but also as a symbol of civilian autonomy (people won't like it if you take it) and of course everyones favorite planet type, the fortress iserlohn, which can just blast enemy ships out of the sky with a superpowered cleansing brilliance with 10times the size and 20 times the damage

Afterthoughts:as a bottom note, most of this goes in the direction of something Terraziel wrote, and which i found quite good, that you don't really research stuff, you just develop new tactics. the research is already there, it's not like you can develop a complete new type of ship in a few days/weeks time (didn't happen in LoGH either), but instead you take the extisting technology (ships) and think of new uses for it
along these lines, most of my suggestions here take that one step further, so that you don't even really build most stuff either (apart from military things like ships, factories and defenses), most of the civilian/industrial infrastructure is already there (obviously military leaders seldomly colonize and develop planets) but you
take and
use the existing stuff. so no building trade centers or reasearch centers or something like that, you just say "ok, this is a really nice trade center you have there, lots of connected trade routes, im sorry but the military needs this now, its war after all"
still, a mixed approach could be even better. so that you CAN actually research new stuff and build things, but thats expensive, takes a lot of time, and happens not often compared to the other option. so maybe you can indeed develop a new kind of ship, but it won't happen in a few minutes, and it will cost you dearly, but still, then you have something your opponent hasn't, and thats not too bad either.
And because the post isn't already long enough (lol..) another thought on that:
it would be sensible to be able to capture enemy structures instead of just destroying them (assault crews and stuff), but that should be an important decision, as, when you come across an enemy planet, which has a huge orbital factory, you can capture it and use it for yourself, but on the other hand, that gives the enemy the opportunity to take it back (especially if you are in the middle of his territory), so if you destroy it instead, you have no gain, but you are on the safe side that he has a significant loss (this all makes much more sense if the structures really are freakin expensive)
to not make capturing things overpowered, it could be only possible if no opposition is left in the gravity well, or it could take a while, other ideas are appreciated. but i think this approach would really deliver the feeling of LoGH more than just build a lot of stuff and blow up a lot of stuff. which didn't happen in LoGH, the blown-up stuff was mostly military ships (of that, really a lot though), and few else.
Soo, this was quite a long post, i'll stop now before no one even bothers to read it anymore

i'll put more ideas into another post another time, no need to create an excessive textflood all at once (not that it isn't quite a large wall of words already <.<

so, im sorry if it got a bit long-winded, but i hope you find something useful in there ^^