In order to spice things up a bit, I was thinking each faction could pick a "Template" which influences what they start with, and perhaps their future development.
For example, if your faction is ex-Imperial Navy, you might start with a few loyal Imperial Navy ships at your disposal - some of your supporters from before the collapse. If, on the other hand, your faction has grown out of a mining colony, you might get a small bonus to all mining income in the long run, and so on and so forth.
Obviously these should tie into a faction's background as much as possible, so don't make anything too specific.
Name: Name of the template. Keep it simple.
Requirement: Backstory and roleplay requirements.
Description: Any relevant description material for the template.
Effect 1: Primary effect of this template.
Effect 2: Secondary effect of this template.
Name: Imperial Loyalists
Requirement: Leader was in the Imperial Navy prior to the Collapse. May start anywhere on the map, preferably near the center (Remnant systems).
Description: With the Empire's Collapse, the Navy collapsed as well. Admirals and their fleets were scattered by fate, fortune and luck, thrown to the solar winds and left to survive. Not all have fared well, but others have managed to find still-loyal planets, and aim to rebuild the Empire alongside the Remnant. With a small cadre of loyal and experienced warships at their command, admirals have an initial leg up of sorts, but maintaining the support of the people will be necessary to stay in the Remnant's favour...
Effect 1: Your faction starts with a small group of extra, highly loyal Imperial Navy warships at their disposal.
Effect 2: You are expected to work towards reestablishing the Empire alongside the Remnant.
Effect 3: Remnant Relations start at "Friendly", but are highly dependent on the morale of your planets. See below;
Effect 4: If you rule with favour (planets have high morale), relations with the Remnant are improved.
Effect 5: If you rule by force (planets have low morale), relations with the Remnant are diminished.
Effect 6: If overall morale + Remnant relations ever become too low, you will be branded a Renegade.
Name: Imperialist Renegade
Requirement: Leader was in the Imperial Navy prior to the Collapse, but went rogue as of the Collapse. Must start near the edge of the map.
Description: Not all Imperial Navy admirals were fond of the Empire during it's waning hours. These were often outcasts and those looked down on by High Command, often responsible for small patrol groups in remote sectors, out of sight and out of mind. Using these patrol groups, however, they have seized outer planets, seeing the Collapse as an opportunity to extract their own piece of revenge on what remains of the Empire.
Effect 1: Your faction starts with a small-to-moderate group of extra lower-quality Imperial Navy warships at their disposal.
Effect 2: Initial relations with the Remnant are very poor, and hard to raise.
Name: Imperial Training Academy
Requirement: Home planet is host to an old Imperial Training Academy. Leader should be a member of, or descendant of a member of the Academy's faculty, and regard it as something to be maintained with the utmost care.
Description: Several planets were host to old Imperial Training Academies, and whilst not all of these academies have survived well, some are nevertheless salvageable. Their training equipment, archives and techniques are easily applied to modern training regimes, significantly improving the combat performance of your crews and soldiers in combat.
Effect 1: All warship crews and soldiers undergo training at the academy for free, improving combat performance. Your ground forces are especially improved over standard units.
Effect 2: Starting planet has slightly lower than usual population, but overall (for all planets during the game) morale is increased. Knowing that crews and soldiers are recieving exceptional training is comforting to your people in these dangerous times.
Effect 3: The Remnant may request use of the Academy, and expects you to keep it in top condition at all times. Allowing the Academy to come to harm would seriously jeopardize Remnant Relations.
Name: Dedicated Miners
Requirement: Faction made up of miners and founded from a mining colony
Description: The inhabitants of harsh mining colonies on the borderworlds, miners are used to living without luxuries and sometimes even basic amenities. They are often looked down on by others (especially aristocrats) as simple and unintelligent people, but they are incredibly dangerous when provoked. As a series of riots on Mars showed, provoking and oppressing the miners is the last thing you want to do. Their experience with the upkeep of mining equipment also transfers well to ship maintenance and repair, and they are naturally very good at maximizing their mining output.
Effect 1: Mining output is increased, resulting in better profits.
Effect 2: Higher mining rates are less damaging to the resource levels.
Effect 3: Morale is very steady - it will not suddenly drop, but it won't often spike up suddenly either - even in adverse conditions. Miners are more likely to band together and fight harder if pushed into a corner than give up.
Effect 4: Miners, when finally pushed to revolt, are far more dangerous than other societies.
Effect 5: Ship crews are inexperienced, but are more likely to hold their ground than average crew. Ship repairs are also enacted faster, thanks to mechanical aptitude.
Name: Remote Science Outpost
Requirement: Faction must start near the outer edge of the map, and be scientifically focused. (Think the University of Planet from SM:AC)
Description: Many remote scientific institutes were established to research ancient alien artifacts from long before the Empire's founding. Whilst many were lost during the Collapse, a few still hold together in larger societies. They are excellent researchers, although perhaps not as capable in war, and have a lower starting population.
Effect 1: All scientific projects progress faster than they would for other factions, unless they are also Scientists.
Effect 2: Planet starts with a lower population than normal.
Effect 3: Faction is less likely to be attacked by pirates due to primarily scientific rather than economic focus, and remote location.
Effect 4: Most warship crews are not very experienced, and more likely to retreat from combat when under heavy enemy fire. Some crews, on the other hand, are diehard fanatics who would rather die than see the brilliant flame of scientific discovery extinguished. It's a bit hit and miss, but you will know the mindset of crews when they are assigned.
Name: Merchant Prince
Requirement: Faction and Faction leader are economically focused on trading with neighbouring planets and factions.
Description: With the Collapse, many saw their opportunities to seize the reins of power. Many wealthy merchant families across the systems had survived the pirate onslaughts, and decided to begin establishing a new age of trade. Whether or not they'll succeed remains to be seen... unlike the MegaCorporations, Merchant Princes are not bound by a board of directors and enjoy higher base morale due to their less-oppressive methods of ruling.
Effect 1: Trade output is increased noticeably. Also benefits your trade partners a little. If both factions are lead by a Merchant Prince, trade profits are further boosted for both factions.
Effect 2: All costs are reduced somewhat, making it cheaper to buy ships, install upgrades in facilities, and so on and so forth.
Effect 3: Faction is more likely to come under pirate attack, due to having ships filled with riches waiting to be plundered.
Name: Pirate Lord
Requirement: Faction leader is a pirate lord, with all that that entails. May rule civilians by force, or planets may be solely pirate inhabited. Morale is unaffected, mostly.
Description: With the collapse of the Empire, pirates practically poured out of their hiding places. Some of them, tired of sitting in the background, seized control of entire planets. These individuals are wildly differing - some are charismatic and daring adventurous types, others are cunning, and some scheming misers who care only about their own profits...
Effect 1: May purchase generic pirate ships and deploy them with fleets.
Effect 2: Generic pirate ships may attack and move anonymously, if in a fleet made solely of generic pirate ships.
Effect 3: Remnant Relations may never be improved beyond "Abysmal" except in special roleplay-related circumstances. (Such as providing aid to the Remnant when they truly have no other option.)
Effect 4: Faction has access to "Pirate Relations", which start out at "Warm".
Effect 5: As long as Pirate Relations are above "Neutral", faction will never be attacked by pirates. Pirate attacks are more likely than normal as relations drop, however.
Effect 6: Tax revenue is practically non-existant, but morale is almost always high. Mining is automated or slave-driven, reducing output somewhat.
Effect 7: May plunder adjacent systems and trade routes for funding, resources, ships and slaves (to increase population). The larger a system's population, the more you gain from plundering. Ships tend to be in poor condition, and may simply be taken apart for extra resources.
Effect 8: Must plunder regularly to maintain pirate morale, lest your subordinates become rebellious. Some may just leave, but others may call a mutiny and attempt to kill you!
Requirement: Faction must be a mega-corporation, of course.
Description: Your mega-corporation owns practically everything. You pay people to work, they pay you for habitation, services, food, almost everything. Though careful balancing of the books, you can only profit! Unfortunately, if you live in a MegaCorporation, it's likely that they see you as little more than a cog in their machine...
Effect 1: Extra boost to tax income.
Effect 2: Base morale tends to be lower and more prone to fluctuation. Worker riots are dangerous.
Effect 3: Accounting and careful rulings allow for cost-cutting for all projects such as ship construction, facility upgrades, and so on.
Effect 4: Must maintain positive relations with the Board of Directors or face replacement.
Name: Religious Fervor
Requirement: You are the leader of a fanatical group, with a very strong following. It need not be religious per se - for example, it could be a faction of diehard Imperial loyalists who will stop at nothing to reestablish the Empire, even if it means wiping every other faction off the map. So be it, for the ends justify the means, at least as far as your ideals are concerned. No matter what, justice is always on your side!
Effect 1: Religious Fanaticism: Your starting population is composed entirely of those faithful to your ideals, and as you're the official spokesman for your ideals they will be extremely loyal to you. The morale of your populace starts extremely high and will be extremely difficult to drop, even if your populace stays poor and lives in squalor.
Effect 2: Serve the Cause: Your morale can drop steeply if your policies stray from your ideals. However, a devout leader who follows the religion closely is likely to enjoy unflinching and questionless support.
Effect 3: Gather the Flock: Your population starts off low. However, you may sneakily send missionaries or operatives to planets owned by other factions to preach your religion and ideals. On a planet with low morale, you are likely to gain converts - this will reduce the population of that planet to boost yours. The other faction's leader may attempt to arrest or kill your missionary or operative and/or block converts from leaving their planet - however, this may reduce the planet's morale further, depending on how much success your emissaries had prior to their removal - religious fervor may snowball unless dealt with, and converts will continue to spread the word if they are not allowed to leave. A successful rebellion is likely to turn the planet over to you.
Effect 4: Grand Crusade: You can whip your population into a religious frenzy and direct them to crusade against the infidel. A portion of your population will devote themselves to holy war. You gain a horde of motivated soldiers, who have no training and sparse equipment, and/or a flotilla of jury-rigged civilian vessels with crappy weapons botched onto them. Expect devotion, but no organisation from this fleet/army, and the ships/soldiers supplied will be no match for dedicated warships/soldiers. The higher your morale, the more people will devote themselves to the crusade. You can disband what's left of the forces later to regain the population you lost calling the crusade.
Effect 5: Giving motivational speeches in-character can help mitigate the effects of morale losses from contraventions of Effect 2. For example, if you can justify allying with a life-long enemy who is a staunch anti-Imperialist to your people in a convincing manner, then they may be wise enough to see what you are thinking. Just be wary - you're going to have to be good with words to pull it off...
Requirement: Your faction is in fact an alien race of some kind, be it humanoid, mechanical, bio/etc. in nature. Your ships, buildings and such should reflect that. It also means communication will initially be... troublesome. Your faction starts at the very edge of the map rather than near the center.
This template may only be taken with GM permission.
Description: Your race is from 'outside' the Empire's layer of the node network, and you have been sent there for whatever reason. You could be an invasion force, inspectors, researchers, explorers... anything.
Effect 1: Your ships and technology are obviously, alien, with all of the pros and cons that implies.
Effect 2: As you are primarily a recon unit, you start with some extra scouting craft.
Effect 3: Morale on human-inhabited planets will drop faster when you oppress them than it would under a human leader. Morale restores at a lower rate as well.
Effect 4: The bulk of your supplies are still in transit and thus your starting population is smaller than normal - after the third turn, you recieve an influx of supplies and population, as the main force arrives.
Effect 5: Adapting another faction's technology is harder for you than normal, but attempts to copy your technology is also harder for other factions.
Effect 6: Your race has trouble using conventional/human orbital structures and so on and so forth. This effect is dependant on what kind of race you are playing.
Make your own! Include as many Effects as you feel is appropriate. As you can see, not all Effects are positive, and others are mutually exclusive. The Name should be simple, the Requirement should tie into the faction or the leader's backstory, and the effects should be balanced as much as possible.