Minor ideas that crossed me mind as I was thinking of SoaSE and other games I played some time ago:
<> Celetania online game was similar to Sins, and ... had a nice structure idea that could see some use in here as well. I forgot it's name, but it's role was to shift "phase jump" speeds between +5x and -5x for all ships performing jumps between your own planets, but can be implemented here as "friendly" (owned and/or allied). The player could choose at will how to manipulate the speed that ships will have when "phase jumping" between his own planets, with a different function button for each "owned ships", "allied/ ships with a NAP" and "enemy ships"; basically making yours and allied ships go 5x faster between ur planets and enemy ships go 5 times slower. Could see some use I guess.
<> Star Trek game series featured the idea of "ship crew", and the possibility to transport crew to enemy (also allied and owned ships and stations) to capture them, or to resupply them with crew should it need to repair Life Sustaining, which if fell under 100% u'd start losing ship crew damn fast, or to repair Engines - not able to move if under 100%, Shields Generator - the percentage of this field represented the speed -below normal speed- at which the shields would recover in case of damage.
<> Repair Stations that would require the ship to go there and be repaired (not from orbit) and also cost you resources instead of own Energy, like in Conquest: Frontier Wars, Star Trek Armada 2, and many more. (This could be implemented to the Starbase, probably a nice replace to TEC's Repair facilities upgrade from the SB, which I believe that lacks any great use as is)
<> Advent and Vasari Pirate forces? Advent and Vasari militia?
<> Set "Quick-start" to also give 1-2 planet bombers to players at start, while the Militia start with hardened positions on critical planets (Terran and Desert) - like first level infrastructure (1500 HP) colonised planets and 1-2 Hangars so to make a better difference between their and Asteroid Militia?
<> better differences between Loyalist and Rebel factions, as stated in the advertisment for rebellion ("each faction will come with it's own ships, each with it's strengths and weaknesses" thingy, because there is really no great difference between the factions, apart from the Titan, the 6 peculiar Researches and the Corvette).
<> Player choosable play styles:
Normal: basic play-style, no pros and cons
Aggressive: a bit more brutish than the others
Pros: Cheaper ships, and ship/building-upgrade Researches (Hull, Shield, Damage only), by 10%, (non-)stacking
<> start with 1 Military Lab; +10% to Tax/Metal/Crystal income, depending on race.
<> win more diplomacy points when finishing missions for others.
<> start with Cannon Research completed, but require 8 Labs to use it; Cannon deals more dmg.
<> ships deal 10% more dmg
<> Starbases come with 1 level Weapons-bank Reasearch completed.
Cons: A bit more expensive Researches for Economy branch.
<> lose more diplomacy points when losing missions for others.
<> ships build times are higher, but have +1 armor and +1 damage than normal.
Researcher: either a bit better bonuses from Researches, or global cheaper Researches.
Pros: Cheaper Researches (20% price cut for Economy branch only) and 10% price cuts for all other Researches.
<> Start with 1 of each Research Labs, or only 1 Economy Lab.
<> 10% price cut to all defensive Structures (except Cannon)
<> 10% faster researches overall.
<> Starbases come with 1 random Upgrade completed (between Trade, Strike Craft host capacity, Offense and Defense).
Cons: Ships have a bit lower dmg/ cost a bit more.
<> Defensive Structures, ships deal 10% less dmg.
Economist: better economy than the others.
Pros: increased income rates from all Extractors and Tax sources, 1.5/2 Credit income from Trade Ports/chain lengths.
<> lower prices for Diplomacy branch Researches by 10-20%
<> start with Resource-Exchange between factions research completed (also with any previous research).
<> gains reputation faster from resource donations.
<> Starbases build with Shipyard Upgrade.
<> lower prices for Infrastructure upgrades.
Cons: Defensive Structures deal less damage, but also cost 10% less.
Fortifier: greater defense
Pros: shorter build times for Defensive Structures, 5-10% cheaper Defensive Structures
<> + 5 more Tactical Slots/planet.
<> start with completed Research for Starbase (this could be a problem with Vasari I guess), or with Cannon Research completed, also requiring the 8 necessary Labs to build it, cheaper Cannons to build, normal damage.
<> Starbases start with 1 level Integrity Upgrade completed (and probably with the one that increases it's HP and Shields by 10% also already completed, the one generally at Tier 6 Defense Panel).
<> 20% cheaper upgrades for defensive purposes (Repair Station, Hangar, Turret and Space Station Researches and Upgrades)
Cons: Defensive Turrets deal 10% less damage
or some bonuses similar to these, above race researches and stuff.
Thanks for reading!