I've got a long one for you but I think its worth the read.
If the player is laying out structures for different reasons then make that gameplay just one part of the game that leads to prefab constuction for later. Maybe challenging the player with objectives to build the ideal resource base (base being a combo of structures), the ideal construction base, the ideal recreation base, ideal population base, the ideal defense base, etc. Once the player has these "ideal" prefabs, challenge the player with placing them in ideal places on the planet. Then challenge the player with different planet types to get the best combination of bases across the different types of worlds. Once the player has a few "ideal" prefab combos of bases for different planet types give the player a gradient of world types meaning that you have an ice planet, a volcanic planet and a few types of volcanic ice/icy volcanic planets so the player has to really think about placing a prefab or taking the time to maximize the planets output by hand designing the base layout.
The same system could be used for combat, the player could start with an outfit of combined arms purchased from the base to take out enemy bases. Once the player is controlling multiple bases they could build an army to dominate the planet. Once in control they could construct an "ideal" orbital launch base and begin construction on their orbital construction facility to start building fleet assets. As the player builds a large enough standing army on a world and a sizable fleet, they get to take their fight to new worlds. Once in control of multiple worlds the player could build warp gates and orbital outposts to move goods and fleets quickly and easily between major areas.
Along the way the player could be researching and upgrading individual structures, base designs (for better prefabs), world terraformers (to increase a worlds total output), deep space mining (begin earning resources for planets that are running dry), etc. Thus allowing them to focus research in the areas and on the scale they see to be important. Finally, instead of asking the player to upgrade each new asset across their empire, make the transition "in fiction" and as player driven as the player would like by making new tech expensive to replace the old tech. If new fusion reactors means higher output, make it pricey and have a base need to be achieving X amount of output to achieve the upgrade. This means the player can choose to make changes to a base by hand or let the base automate a slow increase to achieve the new tech (or even just wait for its price to go down as time goes by). If a new prefab base is designed to achieve X amount of output make a world need to achieve X amount of output to redesign the old prefab for the new one. Again this allows the player to choose how hands on they'd like to be in the process. That way its automated but still requires the player to "tweek" things to get full efficiency. Have it clear when something is outdated on any level be it a structure or a world and make sure their is a reason to have outdated stuff like pirate worlds, junk worlds, slave worlds, etc it keeps the universe feeling organic. A good reason to keep tha pirate world is to keep entire worlds from falling into civil unrest (if you were confused why you need outdated worlds).
Hope this idea gets the juices flowing.