First off I'd like to say I love sins, it is a great game and I fully plan to get two expansions next pay check. That said if they decide to add more expansions or do a sequel here are the things I’d personally enjoy seeing added to the game.
Ideas I'd second
Cloaking (Only if done really well I'd like to see long range cloaking and visual short range cloaking be two separate technologies)
Moons
More races and perhaps Revolting races that can become AI operated empires and new factions
More planet diversity
Better physics in space battles
Other idea
Two new ship classes Mid-Sized, and Super which would flank capital ships in terms of size and power.
Mid-sized obviously would be capital ships light. They would be able to advance but not gain all the abilities like capital ships can nor would they have the excellent cap armor class and would in turn be more vulnerable. I'd suggest mid-sized ships could fill a nitch as hybrid ships able to perform various functions based on specializations and use a simpler three tiered vet system for advancement.
The Super Sized ships would be all in ones probably only good for final late game pushes when you've lost a few capital ships due to their high investment costs. In fact I'd suggest that to build one you have to sacrifice a planet effectively turning said planet for a productive member of your empire into a giant industrial wasteland suited only to the intense manufacturing demands that building a larger them capital ship would require and be a drain on your empire while constructing a super sized ship.
I'd also really like to see Espionage/black ops
Espionage was an element that was totally left out of Sins 1 and I understand the reason for it. However I feel this is a strong element that could add a lot to the game which could also help define any new factions in the game. However I’d like to see this not be a simple remote ability as it is in most games such as the frequent example of sabotaging a mega-weapon but also one that could play into combat. Getting a sleeper agent into a fleet or planet could let them unleash havoc at a critical moment. Imagine jumping in with a small strike force while your agent turns off the defense grid for 2:00 minutes. Allow players to establish smuggling on disloyal worlds allowing them to siphon off production to worlds. I’d like espionage to be an active element with synergy with the rest of the game (similar to the new diplomacy which takes into account relative faction strength, cultural differences, tech levels etc. etc. rather than just exist in a bubble from the rest of the game like the core diplomacy) rather than an isolated new element. Further different factions could have different espionage options. The Advent could probably create sleeper agent for example mind warping average citizens into a 5th column which would come alive when the advent strikes launching rebel ships similar to the TEC tech ability, TEC might be able to bribe individuals into using defective parts so a ship will take damage when it tries to use its special with the more money spent both increasing the likeliness of success and the severity of the effect, while the Vasarai might employ some sort of covert force to manually detonate a one of their EMP like attacks in a specific system. Allow espionage not to be an all or nothing sabotage but way of softening up a system or force for your invasion. As great as I think this would be though I’d rather see nothing done with this then to see it not done well.
Advanced Culture and Loyal is another must. This needs the full diplomacy style over haul. Right now it is overly simple. You send people TV they adopt your culture, even if a planet has been bombed free of all life forms. I thought that Star Wars Rebellion didn’t do a lot of things right, but the loyalty system was one of them. I would really like to see actions, missions and other factors influence culture and loyalty rather than just TV relays and super weapons. In short develop this mechanic and give us tools to manipulate it. Planets with high culture should join you intact rather than forcing you to attack them. Enemy controlled but high loyalty planets should be exploitable in some way. This could tie in extremely well with espionage options.
I love the bounty system in Sins. It is one of the most original parts of Sins and an excellent tool for people to exploit against their enemies indirectly and a huge boone economically inclined players. I’d really like to see more of this sort of 3rd Party Tactics. Perhaps if espionage is introduced there could be a similar systems involving a shadowy organization like Mass Effect’s Shadow Broker whom you could pay off to run espionage against your foes similar to how you can exploit pirates to attack your enemies militarily.
Let me just close by listing one things Sins doesn't need; Land Battles.
I see this a lot on the boards here but please, please , please do NOT add ground combat. I’ve played a large number of games which mixed space and ground combat and every time it has been a very negative point of the game. With space fleets the instances where one would need ground combat should be few and far between. Conquering a whole planet on foot would be ludicrous to try and simulate. It would not be single simple battle, it would not be a simple objective based fight and virtually any ground force should be easily destroyed from orbit. Ground fighting would be guerilla combat to resist the invaders as best. I’d rather see them continue to improve space battles rather then split their efforts. To make good ground combat they would have to effectively make a whole new C&C style game and slap it into Sins to make it on par with space combat. Ground combat isn’t fun and I’d rather see developers put their time on other game elements.