Here's an extra long one, since I haven't posted in so long;-)
I haven't played the beta because it would probably take a whole day to download with my internet connection, but I have seen lots of video of it now. In watch all the YouTube videos on SCO. So I understand it. It's exactly what you would expect, the same thing as SCII on a round ball instead of inside of a box. It's the way to do it in 2018, especially with precedent games like Mario Galaxy. But it can't be any kind of mini-game because that would take far too long with all those planets out there.
So maybe you should think outside of the box of being exactly like Star Control II in terms of distribution of resources. Make this universe mostly barren in terms of resources where only a few planets or moons in each system have the typical mineral resources on them (or any worth collecting). Energy/quests are a what and where they are. Then it can be more like Mario Galaxy, each landing a little arcade game scenario to play out. About half a dozen general ones like "steal/acquire this item" or "eliminate this threat", and then as many "custom" ones you or later the community makes. Have far less landing, but turn that landing game into a mini-arcade game.
A mini-arcade game as a lander game isn't realistic at all. This is "beer & pretzels" or "fun over realism". Realistically almost all of the planets should be barren and all should have and abundance of one resource or another even if they aren't useful ones. But that makes for a pretty boring galaxy. The mini-arcade game thing gives you that aspect to incorporate into quests, which makes the whole quest thing more dynamic, often with a custom landing game to go with the quest. I'm sure it's too late too take this too far in this first release, but this could be expanded a lot in the first major DLC. It would actually "steal the show" from Fleet Battles and be far more of a focus that Fleet Battles in the full adventure game.
Of course, you have to be willing to "surrender to toc" on the realism issue in favor of your own "Star Control Universe". The still somewhat cartoony look, which I've always loved, goes with being a little "anvil on the head" unrealistic. The reality of space is that it is an almost entirely cold and empty place. It's not the best source material to be working with in terms of "realism".
You would probably want at least 3 types of landers if you did something like this.
Reconnaissance (high speed, long range detection/item pickup, science)
Transport (space marine platoon, like Ur Quan fighters on the ground)
Heavy (pure combat, slow and heavily armored, has a missile launcher or some other type of “big/primary gun”)
These are the ones that immediately come too mind thinking of Star Control, you might have 5 or 6 that fit into your game.
As for a lore explanation...
If the Scryve are controling this part of the galaxy, then they would have to be monitoring this part of the galaxy. You can't control an area of space if you have no idea what is going on in it. The image of a single person on some tiny outpost in space is in a lot of sci-fi, you meet Nelix living like this on Voyager for example.
I would think of them as “coast watchers” from the pacfic theater in WWII, but sides had often lone people on islands reporting whatever happened back to military commands. This would obviously be “penal duty”, like being sent to the Russian front could be for Germans in WWII. Nobody wants to be one of these “coast watchers”, so these Scryve are usually in even more of a bad mood than the typical Scryve.
Of course, they also might be more likely to be disloyal... and wherever it goes from there. And then you have these “Scryve Recon Outposts” to explain the basis of where there is so much defended ground around for you to be fighting on. Those are just the spine to give you enough to make it believable, and you can keep expanding the more “populated” planets from there with other “story excuses”.
And then you still have most planets that are “empty” which is comparatively what you have now, but “empty” planets with enough pure resources to be worth going after compared to the “populated” (...purely for whatever the arcade combat mini-game is) are exceptionally rare (like Legendary cards in a CCG rare) so that most ground stuff happens on the mini-arcade game worlds.
Really running with this is probably more than you can do in the first release, but you might be able to get the “spine” of 6-8 different objective/mini games/scenarios going in time for the initial release.