Here's a list of minor things I'd like to request for ES2. Obviously no expectation or hope that these will be implemented, but they're things that I can't do myself that'd vastly improve the game.

I'll sort these by category to make things easy

Modding:

• Prerequisites in Population Modifiers Traits
  • Just a simple thing, but I've encountered situations where it's obnoxious to not have them available
• Prerequisites in Academy State Definitions (It says all of them should work, but only Path Prerequisites work, probably a bug)
  • I wanted to tie the Academy's ability to colonize off of a game setting, but alas
• The ability to add simulation descriptors to any object manually based off of any prerequisite
  • My intended use is to add simulation descriptors to say, the academy, in order to increase their difficulty by giving their faction traits
• The ability to make generic Entity Actions, and specify their effects using Simulation Descriptors or Temporary Effects
  • I wanted to make a thing that damaged a ship and gave them a one turn speed boost :(
• Add duplicates of every hull type, like you did with all the planets, so that we can make custom reskinned versions in faction mods.
• Add the ability to add searchable tags to techs, please, I want to search by effects of the tech, or search for affinity-specific techs.
• Add the ability to add custom buyout options, like with the United Empire's influence buyouts. (I'm aware this is a big task)
• Add a prerequisite for if specific mods are installed
• The ability to make and share modlists/modpacks

Quality of Life:

• Ship Creation Waypoints. PLEASE.
• The ability to upgrade ships into other ship designs that use the same hull
  • Allows for outdated designs to be repurposed :)
• Sending Food/Industry Stockpiles to another System
  • The functionality is already there with outposts, if we could control it manually and use it on colonies, a lot of things would be easier
• Bring back marketplace features for Auctioning and Advertisements
  • The market is boring and not very helpful, this would vastly improve it. Imagine the Lumeris being able to auction systems, and the United Empire putting out a request for someone to sell a hero to them for a very high price.
• Explain the hacking mechanics better
  • Please, no one understands what half of them do or how they function
• Give formulas for things like trade income and food consumption in the description or tooltip
• Put the ship role icon in front of the hull in the ship design menu, it gets really confusing
• Add turret degrees in their description. I want to know what the range of my turret is.
• Add an option for Open Terraforming, Unique Terraforming, Enabling PVP Hacking, Enable Academy Roles, and Enable Academy Colonization. Players have been requesting these for a while!
  • Open Terraforming meaning you can terraform in either direction
  • Unique Terraforming meaning you can terraform unique planets
  • PVP Hacking meaning you can only put sleepers and backdoors on systems (only on players)
  • Enable Academy Roles meaning that Isyander doesn't beg for money in exchange for roles.
  • Enable Academy Colonization as in, they don't actively colonize
• Increase the character limit in text fields
• Add a text editor type of thing that allows us to put icons and text color in our messages and names
• Add a way for the Vodyani and Umbral Choir to destroy the Academy Home System. They currently can't do anything
• Add alliance voting, please, I don't want to go to peace, PLEASE IM MID INVASION.
• Remove behemoths from faction ship preview.
• Add the ability to change out luxuries in system development, in case you make a mistake.
• Separate Hacking and Economy from being in the same view, it gets confusing
• Add a diplomatic option for making demands, and seeing how likely some one is to accept or deny.
• The ability to have match spectators

• Endless Space 1 Moons
• The ability to make custom modules
• Cooperative Hacking Operations
• Harmony faction + new ecologist mechanic
  • PLEASE I JUST WANT TO DESTROY DUST, make them able to buyout and trade on the market with strategics or something, it'd be so cool.
• Sowers faction + cool terraformation
  • More planet types, with a "perfect" planet for every FIDS (plus happiness and population slots). Something similar to tile improvements in Civ, like perhaps custom anomalies, or perhaps a way to upgrade planets (A separate thing from planet specialization)
• Amoeba + diplomacy overhaul
  • Here are some fun random ideas: the ability to enact alliance-wide laws or effects, allong with alliance voting. Some sort of galactic-wide UN council thing to outlaw things. Possibly some fun events like not being able to communicate with faction leaders for 5-10 turns.
• Broken Lords + ground battle rework
  • Maybe not broken lords, but some faction that builds population with dust would be really fun. Some ideas for ground battles: 
  • Ground Battle Rework to allow for strategies, more unit types, and positioning. Imagine being able to tell your Hissho Samurai to go in first while blasting out the enemy tanks with artillery. Clearly what this game is missing, since ground battles feel shallow right now. Just an idea, I think it would be hilarious if the Yuusho became a major faction and this was their mechanic.

Although none of these are ever likely to be added, I'd love to see:

- Complete custom faction creation overhaul. Allow us to utilize minor faction images/appearances when creating our custom factions, or the ability to import upload our own images. ES2 has a large amount of potential for RPG, player creation campaigns that would help keep the game alive. Right now custom faction creation is really just renaming an existing faction and tweaking the perks a wee bit. It's mostly gameplay oriented and isn't very visually immersive. 

- Ship modding. I'm not a modder, but it's always been strange to me that the Endless series games don't allow, or haven't seen a wide variety of starship skin modding. Other strategy games, from Stellaris to the Total War Series, hell even Empire at War, have vibrant reskin mod communities that help visually transform the game into other universes and have helped sustain the communities at large for years. I'm not sure if ES2 is just extremely unfriendly to modding, but if that could be changed that would be wonderful. I mean who wouldn't want such a terrific 4X game set in the sci-fi universe of their choosing thanks to a little bit of extra mod support.

- Sheredyn Ship skin, among other fleet skins (I'm aware, thanks to a Dev response, that they are no longer working on ship skins), however, I feel that this is such an underutilized area of the game, however, one that could be potentially fixed by increased mod support in the above area. 

- More factions, any of the ones listed by the OP would be amazing additions to the game, or hell, I wouldn't even mind some new factions being added. I've loved the new additions, and even though they've had their fair share of issues, they helped make the in-game universe feel a bit more rich and alive. Touching on this, I'd love an actual Lost or Endless faction. Unless there's an Endless Space 3 in the works for some point in the future, it' seems like such a lost opportunity to not add the faction into the game, especially since they've been hinted at so much and depending on your chosen outcome in your Academy Quest, are confirmed to be returning in some form or another. 

- A way to control influence spread. Sometimes I don't want to have it all over the given universe spreading randomly. It leads to an annoying amount of AI diplomacy requests to not passively capture their planet when I have no intention of doing so. 

-Make the Academy a playable or customizable faction in some regard. I mean, they're an integral part of one of your DLC's, with nearly all the assets necessary for a fully-fledged faction except you can't do anything with them other than bargain and obtain an overpowered fleet every 20 turns or so. It just seems like such a waste, and I'd love to do an Isyander campaign at some point. 

-Allow for moons/unique planets/wider range of positive and negative traits for starting planets. And/or for a way to change capital system without having it blown to bits. We're playing as intergalactic empires with eventual access to powers to control space and time, and we can't choose a new capital planet? Or have a couple of moons on our home system? Isn't that a bit weird? Hell, the Romans made their capitols Mediolanum and Constantinople even though they're named after their home city. And they certainly couldn't control space and time.  

- It'd be awesome to construct artificial planet-like structures such as the Academy, or what the Forerunners did with Ecumene and the Halo Rings, or the Xel Naga with every galaxy they visited, and it would fit in nicely with ES2 lore. Once we reach Endless Level in the Technology tree, the actual in-game effects don't feel or look as grandiose, other than an increase in numbers on the UI.

- Please allow for capital ships to carry both fighters/bombers and weapon placements, or increase their slots, or increase the numbers of fighters/bombers while decreasing their stats. I mean it just seems so strange. Lumeris capital ships (far from the most advanced) in the trailers are carrying hundreds, if not thousands of fighters, and yet in-game it's a meager dozen or so. 

- A skill dump for heroes, like base-level combat/economic skill dumps that can be filled endlessly. It'll help with UI notification spam, and make keeping heroes around for the long game a bit more worth it. 

- Options in galaxy generation settings to reduce AI expansiveness/aggressiveness. Since the beta, I've been wary of entering with alliances with any AI faction simply because they're way too expansionistic and will enter into nonsense wars for no actual reason. I understand this is a conquest/victory oriented strategy game, but sometimes 10-20 turns of peace in the galaxy isn't such a bad thing. The galaxy also fills up extremely quickly which feels sort of off? I know this is (lore-wise) a period where so many factions are expanding, and the AI probably is programmed to be as efficient as possible, but sometimes not seeing a galaxy near completely colonized (and in such a haphazard way) would be a nice change of pace. Some of ES2's best moments, as with any strategy games are at the beginning of a campaign when everything is a bit smaller/taller, decisions are a bit more impactful, large portions of the galaxy are sparsely explored, not everyone is a massive galactic power player, and you're not just waiting and slogging toward the next number increase. 

- New anomalies would be a nice breathe of fresh air to planetary colonization, or hell, even more planet types.