Maybe have it so you don't (and can't) choose individual buildings, but you can choose from one of a few "build loops": loops of build orders that represent a planetary governor's choices. (So something like terraform -> agriculture -> terraform -> agriculture -> industry -> science -> repeat.) Whatever the next "agriculture" building is is built whenever that node is reached.

The trick would be to choose a governor whose loop will be right for the planet itself. Say you've got a barren planet with the ruins of an ancient civ on it. The best would be a governor used to barren worlds (say, lots of "terraform" nodes) with an interest in archaeology (a "dig" node), but maybe no governor available to you has that combination. So you have an interesting choice: appoint the one who will maximize the economic growth, or the one who will find artifacts but under whom the economy will stagnate?

Maybe as the game goes on you can choose more complicated loops, maybe finite state automata that can make decisions based on local conditions. In other words, you'd be choosing AI governors, but not hiding the AI routine from the player: it would be right there for them to see.

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.

"In this type of game, it's not that the task is not fun. At first it is fun, when you have only a handful of thing to manage. But as your empire grows the fun tend to go down, and it become repetitive. I have the same feeling when I play the likes of civilization, or even the total war serie."

The solution is to have something more automatic

"What exactly is the point of having detailed decisions for things like build orders if the user doesn't actually make those decisions?"

How an emperor rules ?

By giving order, and doing micromanagement every times it is needed.

So I think a very enjoyable game would be one where you start with a small number of planets, taking every decision, then as the number of planets grow you are able to make "plans", for example if you have ten planets with almost the same set of ressource, you would be able to replicate all the buildings and structures you have build on the first planet in one click.

You would also be able to give order according to some possible events, such as "if there is no more ore on the planet, reconvert it into post industrial planet" or "begin colonisation as soon as the ship arrive if the planet satisfy some requirements"

Each orders or plans would be designed by the player who would also have all the micromanagement power he wants.

I was just thinking, what about having no permanent planetside installations at all? Just having ships of various types, exploiting planetary resources and populations when necessary, but not setting up permanent institutions planetside. Planetary gravity wells are deep, and it only makes economic sense to exploit resources sitting at the bottom of them if there's something there that you can't get more easily elsewhere.

For some projects, there would of course be planetside buildings, but you don't have to manage these. You could just treat them as delays in ship productivity. (Like, instead of ordering a mine built, say that it takes 5 turns after entering orbit for a factory ship to reach maximum productivity. They're building a mine, yeah, but they're not bugging the Emperor about it. If they leave orbit and come back, though, it only takes 2 turns to reach maximum productivity -- because there's already a mine -- unless the planet has been bombarded in the meantime.)

In other words, be the Mongols. Let the planetary peasants cower down in their gravity wells, exploit them for whatever they've got, and lob rocks down at them if they complain.