Disclaimer: I am an idiot, nothing I say should be taken as if I am educated in game design in any way. I am sorry for my poor spelling and grammar. English is my first language but as I said, I am an Idiot.
Personnel.
A dedicated personnel tab in empire management with the ability to manage staff across the entire empire. Hiring quality is based upon your prestige with the faction and personal trading/combat level. Staff could be transferred using transport ships (reintroduced into the game.) where if the station has one available it is auto selected to move the staff to and from locations. The automation with the transport ships should be limited behind management level? So you should be able to also do this manually. Make service crew and marines nameless numbers. They should be able to be moved in bulk and not micromanaged. I remember hiring my first marine I don't remember his name. Having service crew and marines become nameless would also allow the personnel page to move them around easier and allow more focus on your captains and managers.
Captains, Fleets and Wings.
A captain can lead a wing in number determined by their level(as increases.). At high enough level they can lead a fleet in number determined by said level and receives a new rank.(as increases.) A captain that leads multiple fleets should receive a new rank but have a max level requirement. All of this would make me care more about my captains and not want to lose them. I want to invest in my best captains and look forward to being able to add extra ships to their wings/fleets rather than just checking if they are high enough level to set up a random formation.
Wings and fleets should have standing orders for what to do when and enemy comes into combat range (a range set by you, limited by captain level.) Combat range includes all enemies inside it not just those attacking you.
Standing orders include:
Attack priority - Bombers attacking cap ships, Fighter wings attacking frigates.
Defense priority - Fighter wings defending cap ships/bombers, Capital ships dedicated to defending a station and not running off after one fighter.
Resupply orders - Transfer funds to the Fleet account, limited by captain level, that are to be used on fleet resupply. Including ships, missiles, deployables, crew.
Boarding orders - I would not want any sort of boarding automated unless it is ordered by the PC then and there. Eg, you are joining your fleet in combat and order certain ships to board a station then you go back to join the fight while they start the boarding process. There should not be a "board ships at %hp option" however if a ship is targeted for boarding by the PC ships with standing orders for boarding could pull away from targeting that ship, move to targeting ONLY turrets and shields, change to defending the boarding ships over their current orders.
Retreat orders - pretty self explanatory. Ship hits certain %hp/%shields (based on captain level.) they withdraw from combat.
Marines and service crew should "take damage" during combat. As the damage to the ship increases there should be a %chance of losing either a service member or a marine (This should have a hard cap. probably a % of the ships starting crew before combat to avoid having to just restock the ships with crew after every fight.)
Docking orders - When no enemy is within the new 'combat range' ships can be designated to dock until needed and vice versa.
Patrol route - Simple mapping on the map that the fleet/wing/hip follows until enemy comes into their combat range.
Supply line ships - Ships carrying personnel, missiles, deployables that have small ships to ferry supplies to larger ships when no enemy is in combat range. Amount of ships and speed of resupply determined by the main ships captain level.
Ability to set a max station account and anything over is transferred to the player account. Using the empire management page will also show the +% and -% each week/day.
The microchip + Smartchip production tree is too efficient and cheap to produce with high value and demand (Maybe adding an extra material to the final stage of both?). All of the silicon tree could do with a tone down. Scanning arrays are the only mid range Silicon based product that require a secondary material to produce.
Automated miners should not be overly profitable by themselves. They should be used to make your stations more efficient by them mining their own resources.
Solar panels are too efficient and cheap. Adding them to any station removed any energy concern and due to their price compared to other modules it doesn't make sense not to add them.
Nividium could be one of the starter resources for a civilian based economy. The Civilian economy would include Food and medical supplies, clothing, Air filters, Artificial Gravity stuff etc.
The ability to set up trade routes by selecting systems rather than just selecting products. Eg: Right click> select create trade route> select product/products> select systems. I would rather have this than auto trade.
Quality of life changes, balance changes and general suggestions.
Money is WAY too easy to come by. Early mid and late game fly past due to player wealth and lack of punishment for bad investments.
The notification box should be part of a larger page in the Empire tab. Rep gains, orders completed, small events, combat events, cash gains and losses (nothing extreme as this is just for notifications.) All of these should be able to be toggled off and on whether you want them to be displayed in the bottom left and all have an option to make a sound when they come up, eg: Cash gains toggled on to come up but don't make a sound however combat events toggled on to make a sound so you can notice them easier.
Radio chatter is cool but too often and repetitive. I want to hear about cool and interesting events going on in the sector i'm in not just every cargo scan. I like the calls for help or "Xenon fleet breached through the gate." Answering these calls should give little rep rewards and cash if you have a police licence. A xenon fleet event could have the sectors owning faction calling all hands to help and if you ignore it you can a rep loss. The ability to turn all this off would be nice also as sometimes I just want to chill in the quiet of space.
I want to be able to call for help. The higher my rep with the faction im asking the more likely I am to receive it. If they hate me maybe they could join in on the attack too

More options for asking for directions, shipyards, warfs, factories.
Rumors! The addition of the wrecks, abandoned ships, crystal mining, lockboxes, data caches! I ****** love them. They keep me out of SETA afking and actually playing the game. Let NPCs give me rumors of something in this area or that. This could also include the rumor being a trap set by pirates or an enemy faction to lure you out somewhere alone! Maybe they tell you about a great little lockbox somewhere out next to a lonely asteroid to then discoverer a bunch of friend/foe mines hidden on the other side, they then send you a comms gloating "Bannisters send their regards" and the like.
Varied random-gen missions. Eg: someone comms YOU asking for help (rep high enough with faction) that one of their trading ships has just exploded, you get the option to: 1. Offer to deliver the supplies it was carrying. 2. Investigate the site where it was destroyed. (Pirate trap or ship not destroyed and they trying to run off with the ship, offer you a bribe to not inform the faction. Can take or attack them. ect) 3. Retaliate against the factions current enemy wether it was them or not. We all know those Paranid were up to something anyway!
Your ships, stations, captains, managers comms YOU asking for help with something or new orders or little missions. eg: 1. They discovered an abandoned ship on the station, what should they do? (bomb from enemy faction that damages station, abandoned illegal goods, just random ship you now own ect) 2. Wing has a low level pilot on the run with one of your ships. Hunt him down or let him go? (Missions like this should be late game stuff. Empire management stuff.) 3. Enemy trading ship is passing by our area of control, shall we go and destroy it?
I would like my own room in my ship where I can sit and do my important empire things like. Those mining ships aren't going to name themselves.
When I create a design in the Warf/shipyard I would like every ship using that design to have that name.
Non combat fleets, trading fleets and miners where I can give group orders rather than selecting things individually.
Automated exploring really sucks at the moment. There should be an option with a captain of high enough level where you can order them to "map out" a sector with satellites or resource probes.
Being able to define an area for your ships to deploy mines and laser turrets rather than doing them individually.
War mode from the start of the game, Everything happens a little faster to increase the pace of the game so you can jump into combat earlier. The Galaxy is ******, everyone who hates each other is at war. Factions start with extra ships and stations. Have randomized war goals (eg Argon lads randomly get Pious Mists IV as their war goal and start at war with the Paranid. Paranid set war goal of Black hole sun IV in return. They do not have to be even goals. if either faction reaches their goal there is a %chance of peace or both factions fight it out until one is destroyed.) The player would start by choosing their side BEFORE the game begins and then starts in a mid range ship in that factions main hub with a a locked +rep boost with loyal faction and a locked -rep boost with their war goal faction. This mode has special war mode only missions that are unique to the mode. They mostly push towards combat and countering threats/joining assaults than the usual "build my stuff" missions. Rare missions that allow you to betray your faction that do not happen every time you play war mode. It should be easily possible to lose war mode. Fighting a hard fought losing battle is more fun than fighting an easy win.
Reputation is way too easy to get. Anything automated that the player isn't directly in control of should have a massive reduction in rep gained. Level 20 with a faction due to automation in zones I haven't even visited. The rep rewards and levels should be meaningful. Titles, missions, rewards, prices, npc support should all come from gaining rep with a faction. Mining permits, trading deals, station security licence - police licence.
Crystal mining is awesome, i love hunting through asteroid fields. Anything that keeps me out of AFKSETA is great. They could do with a price reduction or made a little more rare to keep in line with the reduced ease of getting money.
Xenon system attack event should shut down the superhighway for the duration.
NPC ships should get a slight bonus to ship stats across the board apart from speed to counteract player ability. It sounds like an awful solution but what else can you do with people micromanaging a fleet of minmaxed ships vs poor old AI.
I like playing with the game rather than just for it. Missions to join patrols or trade convoys (like before where you get the offer to 1.escort 2.join as trader 3.scout ahead.) Playing with the factions and npc ships is cool. Also it would be cool to really feel daunted by the npc factions. Faction owned sectors having 'super fleets' patroling them.
Having illegal wares on board is a nothing at the moment. I just ignore the comms request then fly away slowly. If you get caught carrying illegal goods you should get at minimum a minus to your rep with that faction.
I do enjoy the personal crafting though. Carrying small goods for missions is cool also. Would be good starter missions for starts where you don't have a trading vessel and can shuffle things around for a few credits.
Modifications are cool but confusing.
Factions could tax you and fine you for things. Trading in them, owning stations, mining without a permit.
Research is cool. You could have to deliver materials, products and rare drops from Xenon/Khaak ships to the Grand exchange hyperbase to complete them. Make me earn it! I love teleportation but 40mins is nothing in X game time.
The "Build a station for me" missions shouldn't give you the station afterwards. You could unlock blueprints for doing them as blueprints late game cost nothing or can be cheesed with EMP while earning one early game would feel cool. Lucrative deals missions could be 'Do something illegal and I will tell about a 1.cache 2. ship with expensive goods. 3. ship easy to board. stuff like that.
Random events like certain gates shutting down would be interesting. (Maybe even a super secret rare not in the patch notes event where the inactive gates open for a short time but there is nothing to tell you so its a surprise if you ever see it.)
If you want people to explore out of the hexes put convoys of ships or missions to stations outside of the boundaries to encourage people to go out. Maybe even hyperlanes where you cant see the end and have to explore out there.
Pirates thinking my two energy cells in the cargo bay of discoverer is "Ooo profitable for me this be" are traumatizing me. I have murdered so many of them now. Go find something more expensive to steal!
Stealing capital ships from factions or Large Freighters should make them just a little angry at you. Currently it is hard to be a bad guy when everyone likes you.
Specialized faction wares from Warfs and Shipyards. I had a bug where I couldn't buy mining turrets in Argon prime and had to send my ships to a different faction to have them put on. That was cool. Make me seek out better engines, weapons and equipment.
The encyclopedia needs so much work. Maybe having people "send in" pieces on the offical forums to fill it out and have someone quickily check over / approve them. I am sure you have some long standing community members would would jump at the chance. A little shout out with whoever submitted its name at the bottom in small text would be nice. (Obviously if their name is something like melonbees not cockmuncher9000.)
I really like that you don't get SETA early on.
The property owned Tab should have separate tabs for stations and ships
Thank you for a great game I am really enjoying.