I think we all agree that the story should be non-linear, with the player choosing the order in which they can complete the story objectives.
Aside from that, what I personally want is:
- More dialogue and more story content overall. I managed to complete SCO's main story in less than 20 hours of gameplay, which is simply not enough in my opinion.
- Make the distinction between the main story and the side quests less sharp than in SCO. Currently we have fully animated and voiced comm screens for the main races, and tiny static portraits with a line of text for the "minor" races, and many of the side quests are simplistic, formulaic fetch quests with a few thousand RU or a free module as a reward. I believe that the world will feel a lot more seamless - and fun - when you never know what is part of the main plot and what is a side quest. And please get rid of those nondescript "wrecked ships" that SCO's Scryve Sector is currently littered with. They are extremely unrealistic (how does your flagship's crew figure out how to repair and pilot them so quickly?), they add nothing to the story, and they serve no purpose but to drive the game's difficulty into the ground.
- Harder puzzles for the main story. You shouldn't be able to solve the main story just by following the Captain's Log. And by harder, I don't mean forcing the player to clean out system after system methodically in order to find a plot-critical item (that's just boring), but making the player think - will this item or piece of information help me win the favor of race A? And the storyline where you obtained that item or piece of information may be completely unrelated to race A's storyline.
- More complicated moral choices. Don't just make the player choose between "good" and "evil", make the playerbase debate which choice is the best one in a given situation. And the more choices, the better. And they should have consequences, too, not just a line of dialogue that says that choice A may lead to event X in the future, and choice B may lead to event Y.
- Make the ship editor much more flexible. The player should be able to edit the ship's stats (crew, battery, top speed, acceleration, etc.) directly, rather than forcing the player to choose from predefined modules. The same goes for editing the ships' weapons and special abilities - make a scripting engine that would let the player design the behavior of the ships' weapons and special powers in the editor. Star Control isn't GalCiv, where everyone researches the same tech tree, and has to pick their ship components from that same tech tree. Star Control ships need to have more individuality.
- We also need more user-friendly tools to create our own story content. Ideally, there should be a full-fledged editor that can be used to edit dialogue, comm screens, in-game locations, scripts - everything to create one's own Star Control game from scratch. And that editor should be as easy to run and use as the game itself.
- Finally, I'd hope for more realistic-looking planets. I'd prefer them to actually look like planets, not the B 612 asteroid from Le Petit Prince.