It would be interesting to see episode specific features introduced to gameplay. For example, there could be a situation where the player is forced to coordinate fleets in an ongoing war, which could be used to eliminate puzzle obstacles while pushing back against continuous enemy invasions. The player can gain new fleets via new allies, under which I mean buddy characters acting like fleet admirals, either 'given' by their government or convinced independently. The player has to resupply these fleets by hauling materials to them.
Other scenarios in other episodes would necessitate completely different chores, but it's important that such features should integrate with core Star Control adventure gameplay without burdening the game with complexity.