I'll just get right to the point. This is a list of ideas for improving the game, why I think they should be implemented, and ways they could be implemented into the game
Limited Oxygen Production
I understand that this is a common thought, but in my eyes even long term space travel would have some difficulty producing O2 out on other planets without some source to draw power or resources from, even in a high-level space age civilization. Therefore it might be more interesting to implement limits on oxygen production from the player's facilities, making things like O2 sources and the like even more valuable. Some examples:
Oxygen won't recharge without power. Your levels will be maintained (or perhaps drain very slowly) but they won't increase until power is restored. This will encourage players to keep up some form of power and/or oxygen supply around at all times, as well as be more careful with air supply
Filters protecting your O2 supply from dangerous gases and/or contamination. Kind of speaks for itself but the added threat of contaminated air would make filters much more important instead of something that seems a bit throwaway.
Developing an O2 harvester. A consistent source of oxygen would be important on far away planets, and the larger the build the more important it would be to keep the whole thing full of oxygen.
Thermal Conditions/Other Environmental Dangers
Something that may be a bit extreme or unnecessary but the idea of adding in thermal conditions for high and/or low elevations would be interesting and force players to plan more carefully before collecting from those areas. That bit of titanium will seem a lot more foreboding atop a frigid cliff or on an island in the middle of a nearly volcanic cave. Other weather conditions affecting your site(s) would be interesting as well.
Thunderstorms on Terran or Exotic planets shorting out power generators and such.
Blizzards on Tundra planets creating sudden massive drops in temperature.
Tornadoes on Arid planets that will pick up any resources not inside a building of some sort.
Probably either aesthetic or for difficulty, but the (possibly optional) requirement to use resources to keep equipment in tip-top shape seems like a bit of a no-brainer, as things like sandstorms would deal SOME kind of damage to your base while passing through. This also provides an excellent resource sink once you have things like the Fuel Generator and Trade Platform.
Wear over time would be interesting and add a sort of life-expectancy to most anything the player uses. With the exception of the Habitat and/or Tethers probably.
Damage from environmental and/or other sources would also add interesting challenge to the game, and force the player to adapt.
Certain fragile pieces, like Solar Panels, Wind Vanes, and so on should at least need replacing from time to time after use.
The need to upkeep a base would provide a minor personal attachment to bases on different planets.
Again probably something redundant but it might provide more challenge, making certain research take more attempts or a more powerful research station to achieve. And attaching paths to different kinds of artifacts would encourage players to seek them all out.
Certain things like the Habitat or the Winch might take more than one kind of artifact to suss out of the machine.
A bigger research platform might allow for more powerful or larger research projects.
Honestly this is slightly surprising it hasn't already been included. A rappel would make exploring cliffs or other structures more feasible.
A rappel could be used like a Tether, but without giving you any O2.
Rappels could be attached to the mouths of caves to make them easier to navigate, or to build bases on top of high cliffs.
It would make it possible to modify crafts in space
Being able to build bigger Printers, Solar Panels, Trade Platforms, and so on would be invaluable, especially if that allowed access to new features you couldn't get before.
Upgraded Habitats could house additional players, gain slots, or even become full indoor buildings.
Upgraded Research could take unwanted materials and convert them into something else, like an Artifact (at a very slow rate mind you), or allow higher level Research like other upgraded structures
Upgraded Printers could build new attachments like Radars, Building Components, larger Batteries, O2 harvesters, and so on.
Upgraded Smelters could smelt more at once, or synthesize low-level materials like Compound from unwanted items.
Upgraded Vehicle Bays could build bigger ships and attachments.
Upgraded Fuel Condensers could generate multiple tanks of fuel at once
Upgraded Trade Platforms could allow you to send resources to other bases that have Radar.
Probably not going to happen, but internal structures like full rooms and such would be a neat and welcome addition to the game, providing a nice end-game sink and offering something to give the player a way to really make a home out on those distant planets.
Housing could allow players to pass time and do something end-game.
Greenhouses could allow players to grow sources of Resin, O2, Organic, and so on.
Landing Pads could provide a proper home for Shuttles and larger spacecraft.
Labs could be evolved from Research modules for synthesizing new materials from old ones, or managing robotics of some kind.
Foundries could be built from Smelters for creating compound materials like Steel
Reactors could be used for the end-game heavy power and/or O2 consumption of internal structures.
A radar would be an interesting way to allow players to pick up on the beacons of other players, and give access to Beacon signal changes
Beacons could be altered to give different signals, letting you mark different points of interest (like a source of Compound or an unexplored cave and so on)
Radar could allow you to modify the signal of your base
Radar could also allow you to communicate and command robotics
A form of mold for your Deform Tool would be really helpful when building things like ramps or other specific structures
It could help control how much and what you fill in or take out
You could look at certain builds before you fill them in
Complex formations would be much easier
Something that would be very welcome and a rather nice heavy sink for resources is being able to build/launch objects in(to) space like Stations or other large craft. Bigger stations mean more resources but could be put into orbit around planets and let you do something in an empty environment. It could even provide a neat way to create a goal the player can pursue as well as a reason to collect O2 or build O2 generators. Best part? It would offer them a genuine challenge as the entire thing would require them to use copious amounts of fuel, planning, patience, and investment to obtain a livable area orbiting the planet.
Oh, and as a side note, mod support. Because this game would really benefit from mod support. A lot.