One of the strongest elements of Star Control II for me was the tone. You start out with a stripped down ship with little fuel, arriving at Earth, only to find it enslaved. You then have to scramble for resources, trying to avoid fighting anyone to survive, meeting aliens who are either collaborating with the enemy or avoiding the enemy as best as they can. Desperation and confusion, which then leads to wonder and discovery dominates the first part of the game, and continues to have a strong presence until the end of the game.
Then we have the Precursors, whose ruins and heritage are present everywhere. You get to hear about their technology and bits and pieces about their culture. You also find out about their allies who have either been destroyed or just died out. There is a strong feeling of nostalgia for the age of the Precursors, as their time seems so much better than the time you are playing in. The nostalgia fits so well with a huge galaxy of interesting but mostly dead planets.
Then of course, there is the humour, which is always there to make everything click together. Without the humour, everything would have been so dark and serious! Star Control II is not particularly "dark".
So I'm really hoping that the tone is somewhat similar to Star Control II. I guess that the humour and perhaps the desperation is obvious, but I hope that the nostalgia also carries over. Inspiring the player to "dream" about lost times by giving just enough information and letting them find traces of past glory (or failures) on abandoned planets is fantastic when done right.