I absolutely love and am enthralled with this game, I think Stardock just did an overwhelmingly good job on all accounts, creating a game which is just more than I could ever have hoped for. Having said that there's 3 things I would change.
1. The company being a more visibly active part of the community, having forum discussions with us, and telling us where things are heading. I know this is a rarity but when I see companies and developers do this it is always such a great experience and from my experience beneficial in the long run. People like to feel like they are being listened too, even if they're not.
2. That Stardock would spend less time making expansions and more time fixing what's already there. The current version of Entrenchment still has plenty of bugs and imbalances to sift through and while I understand fixing these may not be a significant source of new revenue, I think it would definitely help "Diplomacy" to be more polished on release. Obviously the more bugs you have BEFORE you start adding new ships and features, the more bugs and problems you are going to have afterwards.
3. The final and most important suggestion I would have made for Sins would be for the balance and battle system to be a lot more dynamic than "rock-paper-scissors". Though I understand their balance decision, making some ships just naturally stronger and weaker against other, having a system like that makes it SO hard for new players to understand how the system works. I consider myself to be a very intelligent person and I've had to spend hours of research just to figure out which ships are strong against others and in which situations. You can't expect every new player to get online and just peruse the forums to figure these little intricacies out, it should just make sense. For example, strike craft are naturally good against capital ships. Why? Is it because capital ships are rocks and bombers are paper? No. It's because strike craft are inherently fast, while capital ships are the biggest ships in a fleet. They have a hard time targetting the much smaller craft who can simply avoid their main weapons and hit them in their most vunerable spots with incredibly agility and precision. Instead of making this a rock-paper-scissors situation, they could have changed it to a more "dynamic" battle situation, where certain ships were good against each other because of their inherent design and design flaws. Strike craft could move so fast and dodge capital ships and be able to hit their vunerable spots in a way that frigates could not. Though frigates could be fast enough to handle the smaller strike craft, and therefore pose a much greater threat than capital ships. Capital ships however would be fast enough to handle the only moderately fast frigates, who would be much more vulnerable to the cap ships etc.
It's still a rock-paper-scissors effect, but in a much more intuitive and dynamic way, and also in a way that can be manipulated to easily switch things around. For example, let's say as a frigate, you sent an emp pulse into a group of fighters, temporarily disabling their engines. Suddenly they lose their speed advantage, making them VERY vulnerable to capital ships, suddenly the rock-paper-scissors effect goes out the window, but you can't really do that in this game. This is just one example of how a dynamic balancing system just makes more sense and is more intuitive to new players. I've talked to a lot of people who tried Sins and liked it, but were just so overwhelmed and confused that they gave up. But can you blame them? Not everybody has the 100s of hours it will probably take to completely understand the game or at least understand it to an extent that you feel comfortable with it, especially when playing against other humans (pvp, the pinnacle of gaming).
The tutorial system is definitely inadequate when it comes to this as well, which is a shame because I think a lot more people would stay if they felt more comfortable with the game.