Maybe like this: you research (progress) better lasers and all ships are auto upgraded with these (+1, +2, +3), same for armour, reactor, shields, scanners, basic computers.

Not so fast. Upgrading all ships can be too expensive because resources are insufficient, not the best way to spend resources (for example, the player might prefer to build more ships) and even wasteful (for example, some ship classes might already have excessive firepower). Individual ships or fleets might also have a higher priority (closer to going into battle, outclassed by enemy fleets, etc.)
Asking the player what ships should be upgraded seems a good idea.

Assuming upgrades are desired, being able to perform them isn't trivial: some might be within the means of on-board workshops and maintenance crews (which only large enough ships would have), some would require transport from distant factories and/or dismantling major ship systems in a dry dock, causing a lot of travel. What sort of upgrade logistics complications could be fun?

Not so fast. Upgrading all ships can be too expensive because resources are insufficient, not the best way to spend resources (for example, the player might prefer to build more ships) and even wasteful (for example, some ship classes might already have excessive firepower). Individual ships or fleets might also have a higher priority (closer to going into battle, outclassed by enemy fleets, etc.)
Asking the player what ships should be upgraded seems a good idea.

The premise is fine, but I do not want to have "ship designs" that you have to upgrade every single time you research something new.

Also, "what ships to upgrade" it not compatible with the game (you have 5-9 fleets made of 20-50 squadrons total which have like 10,000 ships overall).

So... I can use only mechanics which allow things like "upgrade all ships of 'Falcon' hull in the 1st fleet" or "upgrade all ships in all fleets".

What sort of upgrade logistics complications could be fun?

I market the game as "you are the Emperor not a logistic officer", so I definitely want to skip all the logistics things :) Besides, every single 4X focuses on it, I see no point making yet another one that does it. The whole premise is to break from this low level thinking and grasp the game as the Emperor who sees the whole military from "above" and definitely does not concern himself with what ships is where or if there is a supply of toilet paper on battleships :)

To sum it up/clean it up a bit.

- I don't want logistics, even if it's interesting :) But I could go for abstracted/very high level logistics (like "supply points").

- I don't want separate "design a ship" (especially if it means redesigning all ship types every time you get +1 to toilet paper dispensers)

- I don't want "sizes of hulls", each hull is of predefined size (frigate, destroyer, battleship)

- Each hull is unique and has special abilities (there are like 15-20 total, and I could easily invent more, actually had to restrain myself here :))

- Generation of ships is a must I think... First you build Falcon I, then Falcon II and you can't retrofit/modernize to newer generation, you have to scrap these old ones and build new ones (but how new generation is unlocked?)

- Some sort of strightforward upgrade system is needed (+1, +2, +3)

- Some sort of customization system is needed (armour vs speed, accuracy vs rate of fire, laser beam vs torpedoes, reactive armour vs deflector armour)

I think fondly of (but not sure how to make these):

- modular construction, like you build the hull and then somehow attach to it big components (like weapon type, reactor, armour)

- your scientists "designing components", like they invent a new twin gun laser (better than previous twin laser), so actually these components are like completely separate products (a ship is made of: 1x hull, 3x small turrets, 2x big turrets, 1x scanners, 1x reactor), but how exactly it should work... Especially when you build (shipyard) only hull and no components (I don't really have a heart to make the player build these separately and force to keep track what is needed in what proportions)

Player researches new tech, any ships created from then on get new tech automaticly, any old ships get retrofitted in-space, but after a delay depending on how far out from the empire's center they are, but auto-update instantly next time they visit a planet with a shipyard.

I'm liking that one more and more :)

One thing, I don't want to encourage "moving squadrons around for retrofit", it would be useless micro most of the time. Maybe like that, each turn 10% of ships in a squadron are retrofited as long as the squadron was not fighting enemy this turn (in which case it's only 1%) but no less than 1 ship (so eventually all are retrofited).

Then you would have "% of ships retrofited with X component" stat on the ship/hull type screen (I guess I would have to track each upgrade per individual ship, but that's not a terrible problem - except for display/interface since due to the amount of ships listing every single one would be unfeasible, need some sort of aggregated stats).

You can give a player plenty of customization through research: choosing better damage or better accuracy should still impact the game differently. And modules can be made researchable as well; by opening up the option to install a (usefull)module the player's fleet-capabilities still progresses in the game. So only seperated things if you want them to be.

Hmmm, like you have techs like "+2 to damage", "+10% to hit"?

Sure, or going for defensive instead if the player tries to go stay on friendly terms with his neighbours. As for keeping track of each upgrade for a ship, it's a lot of effort for little effect if the player doesn't get involved, i suggest adding a small (resource)cost to upgrades and then letting the player decide how many upgradelevels a ship should miss before being upgraded.(add different upgrades together or have the player decide this for specific categories/systems like weaponsystem when it's behind 2 levels but computersystem when it's behind 1 level since it's so cheap to upgrade.

Sure, or going for defensive instead if the player tries to go stay on friendly terms with his neighbours. As for keeping track of each upgrade for a ship, it's a lot of effort for little effect if the player doesn't get involved, i suggest adding a small (resource)cost to upgrades and then letting the player decide how many upgradelevels a ship should miss before being upgraded.(add different upgrades together or have the player decide this for specific categories/systems like weaponsystem when it's behind 2 levels but computersystem when it's behind 1 level since it's so cheap to upgrade.

Hmm, it makes sense...

So, you have levels of systems (weapons, reactor, scanner, shields, computer, armour) these are invented via techs system (research). All new ships always come with the best available (obvious). It's tracked per ship.

Then you have "upgrade/modernize" screen on the fleet page. You decide there an upgrade policy for each fleet (you have like 3-9 fleets total). And/or you have a modernization for each hull separately (per fleet).

I can see it work two ways (actually three :)):

- first you have "modernize" button next to each hull type (per fleet), when hovering it shows you the cost

- second like you described some more complex panel where you set upgrade policy for the whole fleet (affects all hull/ship types) then you have a check button next to each hull "never modernize" (those hulls will not be modernized - useful for old outdated ships you don't want to modernize and just wait for them to die out).

- third just like second but separate upgrade policy for each hull/ship type (it might get hairy soon here...)

This would make best sense if the cost of upgrade is same no matter how outdated version is currently installed (like newest sensors always cost 10 credits).

Also some upgrades should be very expensive (like replacing armour should be quite an investment (30% of base ship cost).

- first you have "modernize" button next to each hull type (per fleet), when hovering it shows you the cost

- second like you described some more complex panel where you set upgrade policy for the whole fleet (affects all hull/ship types) then you have a check button next to each hull "never modernize" (those hulls will not be modernized - useful for old outdated ships you don't want to modernize and just wait for them to die out).

- third just like second but separate upgrade policy for each hull/ship type (it might get hairy soon here...)

So, which of those you recommend?

With "per fleet" you mean that vague fleet mechanic you have? I never realy got what it's purpose was, but it makes sense to tie upgrades to fleets if you have fleets, especially if seperate fleets guard borders with seperate neighbours.

Quick question:

Let's assume a system where each fleet/squadron/whatever has specialization/special bonus/equipment. Like "Hardened shields" or "Advanced targetting computers". You have one such bonus active at any time and you can change it. How to make it so the player can't switch it back and forth every single turn?

Note it's a 0/1 system (either the bonus is in effect or not).

With "per fleet" you mean that vague fleet mechanic you have? I never realy got what it's purpose was, but it makes sense to tie upgrades to fleets if you have fleets, especially if seperate fleets guard borders with seperate neighbours.

Yes, that one. A certain fleet protecting a certain border is the important part here (I want the player to build fleets with that purpose in mind).

BTW, if you are super bored here is the explanation how the fleet system works (7m)

Personel that needs rest to restore energie? Someting along adding 1 energy(or motivation) every "off" turn, losing 1 energy every "on" turn, having a max 5-10 energy and losing 1 energy for switching "on".

Personel that needs rest to restore energie?

That would be close to Sid Meier's Starships core mechanic?