Great ideas you have, but i'm not sure if the developers would agree as you already have a mothership in orbit don't forget. No need to build what is already there, just adapt what you have and do it in half the time.
Operational control of the base marines or the archaeological survey team can be an auto function with no need for the player to be involved. You would just need to build a barracks or upgrade the scrubber drones locally to a new level and have some way of having the science team assembled in the first place through an upgrade or a seperate building, Interplanetary research and expeditions I suggest.
This would be a truly optional quest secondary to overall mission and does not detract from the original gameplay for building your settlement, in fact it improves it in some ways. Besides, it would be great to see the marines in action against the plague spores that infiltrate your colony, before they get the chance to infect anyone in their path. Can you imagine what sort of conversation would be had between the survey team and our illustrious science guy onboard the mothership? I can with a wry smile!
Maybe they have already thought of military drones that can be offensive rather than only defensive?
I look forward to seeing what they release on the next update. As you said, regardless i'm having fun playing it!