I want to see the game as a roguelite. Star Control has tremendous potential for this due to its unique 1v1 skill-based combat system. The success of Hades, Risk of Rain 1&2, Slay the Spire, Dead Cells and the like should tell you that there is a lot of demand for well-crafted skill-based roguelites.
In turn with a roguelike approach you allow yourselves the capacity to explore multiple stories in an emergent order that does not tire the player who does not have a lot of time to explore a whole galaxy, or patience for flying to and fro and scanning planets, which by itself is something that is not engaging at all.
Way I see it could be done, you create an "Enterprise-style" scenario, where the Star Control tasks the player to boldly go where nobody has gone before etc. Perhaps there is an overarching goal, such as reach so-and-so mysterious signal through an unstable wormhole which always takes you somewhere new in a sector etc.
Each run, the player will start with a new ship and will have to go through a number of encounters/solar systems. The normal encounters would be things like recruiting alien commanders, new ships for their fleet, ship upgrades, more crew, or *resources for earth to exploit etc. There should almost always be a choice for a player to make on what to take with them however, this is really helps to keep a player engaged.
All these new acquisitions would become part of the player's build for this run and the more they manage to combine their choices,they more powerful they become.
And of course, there will be enemies to face. Either before every encounter like Gunfire Reborn, or perhaps an either/or case like Slay the Spire. The enemies will be standard SC combat, with a number of elites and a number of bosses (typically 3 in ascending order of difficulty) which the player will have to defeat to complete a run. All this with a main difference from standard SC:O. Afterwards, there is no way to reload if things go bad. All results are final. Any crew lost is not recovered until the player find an event that helps them do so. And if they lose their main ship, that it! Player will have to reinitiate their run with a new ship.
However this doesn't mean there will not be a consistent story behind the campaign, and this can be told during exploration, as well as after their death and rebuilt of a new ship. I urge anyone to take a look at how Hades does storytelling as it's honestly brilliant and surprisingly engaging, even though the story is drip-fed in between runs.
*Planetary resources would not be harvested by the player typically, but rather marked for earth to claim. This way after the player inevitably dies, they will have a way to use these resources as permanent upgrades for all the rest of their runs.
I really wish to see a SC game with a greater focus on combat, which is not cheapened by free crew refills and very little player agency. There is a tremendous potential to reuse the engine you already have to make a killer SC roguelite.