The overall experience is solid. Some clear issues persist that can be fixed with work.
Upgrades, Skills, and Pre-Game RPS.
There is too much RPS right now, largely because of skills or ships that are useless in some situations and required in others. If you have morale damage and are fighting space-marines, its literally useless. If you do not have enough sensors and are fighting DE, it can be a nearly certain loss.
This is easy enough to fix by granting additional choices after you know what faction you are facing. The simplest version of this is to have upgrades/skills chosen after you know what faction you are fighting. This should allow people to feel like they are making interesting decisions, and be the smallest change for the most payout here.
Ship Variation and Upgrades
This is a minor issue right now, and does not need to be addressed. Because of how upgrades often work (applying to the whole fleet), you are often encouraged to use very similar ships. People like more varied fleets, but they are more difficult to play and are not supported by upgrades much. I recommend some stronger synergy effects to increase variation in fleet composition. Ships with unusually high turret count (or range) as defenders, non-stacking AoE buffs, or additional sources of important but limited use effects like rallying, scouting, or fleet synapses. Even if it doesnt fit the lore entirely, adding these should be good for encouraging varied fleet composition.
Faction Specific Feedback
IG, Chaos, Tau
No clear issues. Functions as needed with some unique personal flavor. There are no complicated structural aspects for balancing them.
As established by many, cannot do there job. There is something of a basic calculation in a game like this. Difference in range times the time to close, times the longer ranged guys DPS. This is what the shorter range fac needs to get through to deal damage.
A critical problem for Space Marines, is that they cannot get through that and still be functional enough. Right now I would say Space Marines are sufficiently weak, that they could even be immune to critical hits and still might not be good enough.
My personal recommendation here is to add some range to them that will enable them to close. How to do this is complicated, what would fill that role? Perhaps if their lances were literally 150% their current range, acting as a support weapon so the entire fleet's lances could together try to snipe out engines so the fleet can close. Even if they are not primarily a long ranged faction. they need some of their tools to have that range to enable them to function. As we have full fleets and the ability to focus fire, tools don't have to be as strong as many might expect, but they still need to be there.
Eldar using the terrifying combination of both speed and attack range. To speak frankly, this is a huge mistake. I know you are copying from an existent lore and set of systems, but their design is at its core an issue. Speed makes range more valuable. They seek to maximize both together - DE doing this while also harming the enemy's range. All Eldar have the most powerful movement abilities in the game, allowing smooth and efficient 4k dashes with frequency and good and optional turning.
This is not a set of traits that lends itself to having weaknesses. You can crank their DPS down and have them lose on objectives, but this isn't fun for anyone. Instead, I am going to make some fairly extreme recommendations here, based on keeping flavor.
The larger problem first.
Have their Cloak also diminish their own vision range as well as the enemy's. Make sure their escorts have a sensor ping, I dont recall if they have one, but they did not need it before.
They still get to dictate the engagement, and reveal the enemy. Their ships still defend themselves, but lower sensor range means that they have to express some vulnerability to harm the enemy. Right now they can basically be immortal kiters if player well, and are just frustrating. You can use skills or upgrades to cover getting information.
There are many other solutions, but DE need to be dealt with vigorously. They have the potential to suck the fun out of the game for many people, and thats just not really acceptable. Solutions should be related to encouraging them to close on the enemy (lower range works too, honestly), or to de-stealth.
Powerful, but glass. Fleeting, but pretty deadly. I only lost 1 game with Eldar, and it was to necrons jumping on me and exploding.
Eldar do not really need to make tactical decisions, their speed lets them react to nearly everything. Their range lets them ignore consequences nearly as well. My solution to this is to slow down their turning, forcing more of a decision and allowing more counterplay by the enemy.
Halve their turn-rate, literally (maybe not for escorts). Halve the decay-rate for Holo-fields, so they can spend more time stopped but turning if they need to without instantly dying.
Re-balance around new values (though I am not sure they will need significant changes).
Terrifying balance here. The shortest ranged faction, and also the slowest (sorta), while not being that excessively Tanky.
Currently, they are balanced in a very extreme sort of way, you have to use their boarding boats to win. Literally. More powerful boarding, less powerful everything else is a very dangerous sort of balance to have. They win hard, they lose hard, and their factional choices are a bit weaker than most. Solutions for them are a bit complicated - they do have their strengths, but their weaknesses are quite extreme.
As lame as it sounds, I would probably just recommend some tweaks here. Perhaps 25% more health and shields on all ships except escorts, 25% worse boarding-pod effectiveness, escorts get heavily increased base speed. This would give them more chance to engage on an enemy, which maintaining factional traits. Tentacles also likely should have size variations, as they are an incredibly bizzare extreme case weapon when used on escorts.
Trying to manage a swarm of those escorts without having them ram each-other is a tremendous pain that other factions do not need to deal with. They are the slowest ships in the game, and can only travel faster by spamming a ram-dash that is very prone to making them crash into each-other. Truthfully, I would likely much rather have the escorts have no movement techniques, a significant increase in speed (perhaps +50%, still making them the slowest escorts in the game by far), and a drop in cost - just to make them more generally usable.
Tyranids also truly want an improved sensor technique similar to the ping escorts in most other factions get, so they can have tools to respond to stealth heavy enemies.
Orks are generally well designed, but somewhat overtuned. They are a nice and easy faction with a few valid builds. Their most powerful builds could use some modest nerfs.
I don't know Mars priests well enough to truly comment. I will instead talk a bit about Nova-Cannon spam here.
Nova-Cannon spam is powerful, but does not destroy the game. Truthfully, I would encourage it to be less extreme by halving its damage and making it infinite use, but I understand how that would go against other balance decisions.
Being the Nova-Cannon. Necrons have insufficient build variety. Like Tyranids with drop-ships, their dependence on a specific gimmick weakens the faction. General buffs, especially to regen would likely be ideal. They are in lore able to heal and come back, but in practice they play as all or nothing glass cannons.
There are some other bits of feedback, but this is most of it. I am curious how the rest of the community feels about some of this stuff as well.