The main things this game lacks IMO are:

Structure
Information processing

Because it's so free and loose, you have no real connect with other civilizations. In Civ V there's pressure to rush out wonders before someone else nabs them. In Civ BE you could be the only person ever to research a low-level wonder, or you could focus your tech on reaching it only to find out that everyone else had the same idea.

You're also bombarded with tonnes of options and no way to sort or filter them for evaluation. In civ V: Do I build a logging camp here, or do I clear this out for a farm? Actually, I might just drop a trade camp... In BE: Do I build a farm or a manufactory or a terrascape or a biowell or a generator or or or or.........
Similarly, in Civ V you're often given a strong impetus to shore up some part of your civilization - you're falling behind on science, so you start popping libraries and food, or oops! Your army's too big, better get those markets out. I never felt like I needed to shore up this way in BE, so I always felt aimless.

So having rambled, I'd like to see:
Information:
Improved ability to look over the tech tree for synergies, e.g. "which techs will let me get the most out of my farms? I have a lot of fruit - what boosts plantations and fruit?"
Diplomacy screen restored to at least Civ V levels of functionality- why can't I tell at a glance who has titanium to flog me?
Tell me if a city I have a network in has a ♥♥♥♥♥♥♥ spy suppression building.
Split off orbital from non-orbital units.

Structure:
Here I think the quest system would help. Lock things off. Reward me for performing tasks. Tell me to collect a bunch of titanium and give me a lump of production as a reward. Have the Supremacy cyborgs clamour for thorium reactors in every city, then boost my culture or health or Affinity for obliging. Lock off tier 2 techs until I research 6 tier 1 techs. Offer bounties for the first player to achieve various goals. The dirty secret of game design and poetry: total freedom is rarely a benefit.

Also:
Strategic resources seem direly underused. I always just flogged them to the AI (who would of course buy whatever I was selling.) Apart from building top tier military units in the late game, I never lacked for any of them.

I guess some of these are a bit outside scope, heh. Still: More quests, more competition, better utilisation of strategic resources - make most units and more buildings need 'em. I want to agonise over whether to dump my titanium into processing plants or missile rovers.

For me, the little things bug me...
-Retrograde thrusters should be standard. We had more than a thousand sq kilometers accurately mapped out for the Curiousity mission touchdown. I can't imagine our ability to find a favorable landing zone would have diminished in the future.
-Why no ability to assign a military escort to trade units that travel wily nily through hostile territory?
-I don't see why we would need to study any new technology to understand the concept of a trade route. Tie the number of trade routes to city size and make the trade route building a bonus for energy and production. Maybe the capital starts with one route and all cities gain a route at size 10, 20, 30, etc
-Up the trade route reset option to 50 or more turns.
-If harmony spreads its influence to a tile containing an alien nest, they should have a use for it, could be a simple bonus to science or maybe a +20% to unique harmony unit production. Just for the sake of balance, maybe the other affinities could use them too. Purity might have canned hunting trips while Supremacy might build arenas offering gladiatorial entertainment. Another idea is making them affinity specific wonder level worker upgrades, making them pillagable and not rebuildable. You will have a good reason to put extra defenders around it.
I'll think of more...

Okay, I don't know if any one has said this but I think, once you unlock the planet carver and have one city with all the orbital coverage add ons, you can pretty much destroy anything anywhere at anytime. Playing through single player, I destroyed 4 cities in 4 turns just by sending two planet carvers that took 3 turns to make each. That's OP. Think of a fix for this maybe? Thanks.

Revamp the Affinity system entirely. Base points on certain actions instead of tech progression, and restrict certain techs based on affinity level. Destroy nests and build terrascapes, gain Purity points. Build preserves and peacefully harvest Xenomass, gain Harmony points. Disregard health and acquire heavy industry? Supremacy points for you!

Having the AI more predisposed to work with acolytes of their affinities would be great, too. An alliance of Purists facing off against the xeno-loving scum would be delightful, and all the sabotage, civil strife, and assimilation that would come with any gains on either side would be so much fun to explore.

I think the quest system is a great framework - but it is so basic right now. We need more quests with arcs (as opposed to do X, receive Y).
Simple example:
1-Build 3 terrariums adjacent to each other.
2-Protect the tiles from a spawned alien attack
3-Give all 3 tiles +1 culture and +6 energy (remove the upkeep), get (small #) purity points, lose (small #) harmony points and supremacy points
flavor the quest so that it is the construction of a self sustaining national preserve or such.

The quest system is really what gives the player the ability to sculpt and feel like they are telling a story of civilization - so make it so (if possible, it would be great to end them with quotes like with techs... but that might be too much for a simple mod).

I would like to see some more penalties for negative health such as at -20 -25% miltary strength and at -1 unhealth 20% less yeild from trade routes and at -10 50% less yeild from trade routes.

I'd like to see sats appearing from mid-game onwards. probably make the city coverage Zero and only expand it though the launch complex.-this is something that would work from an immersion POV, not necesary but in my wishlist-

The miasma repulsor is too powerfull, too cheap and too early. it'd need to be further upweb and the miasma removal (worker) closer to the surface of the web and probably not dependent on harmony, since it will be used, chiefly, by non harmony facions.

The trade routes (harmony) should probably be able to bypass miasma at the proper level, not sure if doable, but I've heard it as a complain.

The purity scout immunity needs to go.

Miasma, if possible, should have some detrimental effect on non harmony cities (not surei if doable) but as it stands, it is a poor man's xenofungus and it shows.

Fix the affinity quests that require you to build certain buildings in your capital regardless of whether or not that's possible to do so because of the resource restrictions (ie: Biofuel in landlocked capital).

Make Biofactory more like other similar buildings by not requiring both petroleum and chitin to be near each other: probably just make it require chitin and buff chitin.

I don't know how much your looking into what other mods are putting in but the enhanced wonders mod adds some really good changes to them. maybe look into his balances and see if they work with your mod. Maybe making an alliance in fusing both mods. As of right now i think it works great, some of the things he added is making the mid-late game wonders need geothermal. This makes the slavic a great nation to have during that period because of the double geothermal. Kind of like the russians with double uranium. which in my opinion makes both your mods have great synergy.

I posted this sort of thing elsewhere w/rt future expansions, but maybe it'd be better suited here?

Make it so technology doesn't give you as many XPs toward an affinity, especially with the middle- and outer- ring techs that currently can be worth up to 2 entire levels by themselves. Instead, you gain more points by how you play, by constructing certain buildings, or accomplishing certain objectives, and so on. Make the player embrace their chosen affinity and be rewarded for it.
Perhaps you could even earn negative affinity XPs for certain actions that are extremely opposed to a virtue. Currently there's nothing stopping you from taking as many levels in Harmony as you like even as you rampage across the planet, dispersing miasma, slaughtering the wildlife, and terraforming the planet to make it more like Earth. It's a little silly. I'm not quite sure how this should be implemented though, or even if it would be fun to deal with.

The gap in strength between units of different tiers of affinity is absurdly huge, and should be substantially reduced and/or have more tiers added between. A slight tech advantage shouldn't turn into an instant rout because one dude's units are 50-125% stronger than the other dude one tier below. Perhaps make it so that each affinity level (of your highest-level affinity) that does not move a unit up a tier increases that unit's base combat strength by a small amount, making the transition more gradual.
For instance: Soldiers would become Marines at Affinity Lv1, and then for Lv2-5 they gain 2 base strength until they become Brawlers/Sentinels/Disciples at Lv6, with 24 Strength. The T3 Marines would then gain 4 base str per level until they become their T4 counterparts at Lv11.

Expand on naval combat. All we've got are Gunboats and Carriers, which although offensively powerful, are very vulnerable to attack and unable to take cities. Anything that fires upon a Gunboat kills it almost instantly, and this goes double for Cities and Krakens. Our only option to keep them safe is way, way late in the game once you reach certain affinity levels and get amphibious units. Even disregarding the overabundance of Krakens making naval combat a perilous, grindy, and expensive affair, there simply isn't much reason to build a navy if a land war is an option. We need some melee ships that can actually fight and protect the Gunboats, and help take cities from the high seas. Why the hell this feature was removed transitioning from Civ V to BE is beyond me.

Better city management. More than anything I just want a "Stop City Growth" button back, but I also want to see weights and limits to how the governor assigns tiles. Maybe I want to focus production, but not go below 3 surplus food per turn. Maybe I'd like to see a city that focuses mostly on Science but also, to a lesser degree, on Energy. Maybe I want to ensure the city doesn't get more than a certain amount of food per turn, because too many of my tiles have high food yields but I don't want to shut down the city's growth entirely. As it stands, city management is a mess of micromanagement and a pain in the ass.

Firaxis made a selling point of how there would be synergy bonuses depending on how you assigned your points, and you'd be free to distribute your points evenly if you desired. However, I still feel compelled to throw all my Virtues in one or two trees exclusively, because it's too costly to get out of the first tier of a third or fourth tree, and usually not worth the expense to try. Perhaps have some virtues "bridge" into another tree, so that for instance taking a certain T2 Might virtue would allow you to connect to a nearby T2 Prosperity virtue, and continue into deeper Prosperity virtues from there.

I want to see Energy nerfed in some fashion. Currently it's way, way too easy to get well over 50 EPT and always have enough Energy stockpiled, at all times, that you can just expand forever and purchase a ton of buildings in every new city to get them running productively within five turns of their founding. Or tech up to a new affinity level with some fancy new hardware, rush-buy an instant army and march forward. Or both! It's not like I won't have all that energy back in a few turns anyway, right?
Perhaps we can have more things that we need to spend Energy on, or perhaps certain money-making tools (such as, oh, Supremacy Level 3) can be weakened or removed entirely. Maybe make the player unable to stockpile more than a certain amount of Energy at one time - to be increased depending on certain factors you can access as the game goes on, of course. I don't see this being a simple fix.

City strength needs to be nerfed, and their hitpoints buffed. For the most part they can vaporize anything of an equal tech level, but they die easily under bombardment. If there are no units nearby, the city falls easily. If there ARE units nearby, the city (or more likely, multiple overlapping cities) acts as a ridiculously powerful area-denial field.

Firstly, I agree with every change this mod has made so far except for Rejinaldo being able to move after attacking, it reminds me of the Keshiks in Civ 5 which were fun to use but were OP beacause of that ability.

Regarding health, I actually don't think the health sytems that bad at the moment, It can be tricky staying out of negative health early on In the game, but at about turn 150-200 I usually have about +20 health and about 9 cities, so If you wanted to discourage city spam I think the negative effects of founding new cities needs to increase along with -10% production when in negative health. I would also suggest increasing the effect of the profiteering vitue to 1 health per trade route now that the number of trade routes per city has been reduced.

I also think that in the vanilla game the upgrades for military units are unbalanced and extreme, I was able to one shot my enemys navy one by one with my cruisers (28.8 strength) vs my enemys gunships (7.2 strength), the strategic strength upgrades you get are good enough that I don't think units need to get +10 strength each time they upgrade.

I dunno if this has been mentioned, nor do I feel like reading through all this. BUT:

Spamming 'establish network' with spies needs to stop giving intrigue: Probably with a hard cap of intrigue level 1/2

Could you add an option that balances Free Techs. If you could only choose Free Techs that are leafs it would prevent the stupid OP tech slingshots. Some of the slingshots you can do are plain stupid ... the equivilent of picking up a Modern tech in Classical era.

I don't think this nerf should be applied to Spy Tech Stealing just yet ... ironically that could make Spy Tech Stealing OP as Spies would only be stealing useful Techs for your win condition. I personally think that Spy Tech stealing shouldn't be an option until later in the game, but that's just an early impression.

Some other suggestions for discussion:

The ability to switch off Progenitor Ruins and restrict Affinity leveling up to techs only. This takes the randomness out of the game. 2 free Affintiy pops early on could be worth as much as 10-15 turns in the end game depending on your win condition. That is too OP for such a random feature, especially in multiplayer.

Limit the ring of influence around stations to 1 tile only. 3 is just stupid. Why they included such an infuriating troll feature I've no idea. Also if your city expands to the Station tile, the Station is destroyed (or annexed into the city). Most stations suck anyway, so maybe a buff on the Level 2 and Level 3 outputs of Stations?

Reduce the strength and aggression factors of the Sea Monsters (forget their name) ... gunboats are hopeless against them, and they attack every time unlike land aliens. Since you cannot heal gunboats outside of your territory (I think / assume), they are useless at exploring.

The ability to switch off certain of the Spy options. I need to use this more to fully explore it, but I shouldn't be able to Coup an opponents capital city as an afterthought. I wasn't even trying, I just said, "coup, yeah, why not give that a go" ... 7 turns later I just take their cap.That is just plain dumb.