The player builds (or chooses) the ship, the interior, the crew. The player chooses where to go, what missions to take, who is on which teams, who sleeps where, and you can directly tell crew members to do specific tasks/social things, either for its own sake or to affect a mission/another crew member. There will probably be other things - direct piloting, wandering around the interior of the ship, etc.
This is a bit deeper than it sounds, because there are a lot of conflicts, options, and loops. For example, as three missions progress, a beginner might be faced with a conflict as two of those missions require going two different places to advance/complete them. A more advanced player would see it coming, and allocate teams differently or pay special attention to one team to make it advance a little faster, meaning the two requirements fire at different times and both can be completed. An even more advanced player might choose to give one of those missions to another ship and take a different secondary mission for this ship, one which can be completed by traveling to the same place.
Similarly, secondary missions such as thruster optimization, training, upgrading computers, establishing local connections (both personal and technological) will add more play for high-level players that want to optimize. If you start upgrading your thrusters now, you'll have an extra 30% thrust when you go to land on the planet to finish off the scouting mission, which will make that both easy and fast...
Anyway, that's what I've been thinking. It's still a little nebulous.