Currently, only some Chaos and Ork sub-factions have unique skills and abilities. I think its safe to say most people want more of this. Farsight Enclaves and Ynnari are the most prominent ones in my opinion. Aside from those, i think all races should have atleast 3-4 sub-factions with unique skills.

White Scars: They like going fast. Very fast. They could have a skill which increases their speed or gives them more energy. As an, ability maybe something that increases the speed of ALL ships for a small time.

Farsight Enclaves They are somewhat braver and a bit more eager for close combat. They could some abilities that increases their boarding capabilities.

Ynnari I am very suprised that this sub-faction didnt had one. Resistance to moral damage or troop or ship regen maybe?

These are just 3 examples i came up with. Please, give us more sub-faction skills

@eliphas
The Ynnari most defiantly should have access to an ability which regenerates troops.

I had been avoiding talking about this, because now I have no proof, but when the game was in the beta you could actually open many of the skills files in a text editor because they left the engine-readable files unencrypted. Once the live game came out they removed all the unencrtyped versions of the files though, so now no one would be able to see those anymore. Anyway - during the beta I perused these files quite a bit, and I saw that while they weren't hooked up, all of the Space Marine factions also had at least names and some values for a single sub-faction ability each. They were all thematic to each of those sub-factions and unfortunately I don't remember most of the names, except maybe Ultramarines which I think was called Primarch Kin or something like that (technically all space marines are primarch kin lol) and Blood Angels was Red Thirst.

Anyway, obviously these extra abilities could have been canned with no plans to implement them, but more likely than not in my opinion since people are asking for them so often I would bet that Space Marines will at least get these some day.

Some IN sub-faction ideas copied from an older thread, some of the ideas are kind of obsolete, but would be definitely cool to see some sub-faction variety (even if it is optional).

Battlefleet Gothic: Poster-boi fleet. They have specialised heavily in carrier-based fleets in order to better counter the threat of constant raids from pirates in Barbaros Costa and the ever-present threat of Chaos so close to the Eye of Terror.

Unique Upgrade : Auxiliary Ordnance Corps: +1 Charge for all carrier squadrons
Unique Skill : Ace Pilots: Fury Interceptors gain a +20% Evasion Chance, Shark Assault Boats and StarHawk Bombers gain a +10% Evasion Chance

Should make carriers somewhat useful with this faction, since you get a much better chance if landing key strikes and (more importantly for MP) having your scouts reach their destination without fear of interception.

Battlefleet Solar: One of the oldest and proudest battlefleets, they get all the best equipment and are heavily drilled and disciplined, for they are responsible for defending the last bastions of man in the Sol Sector.

Unique Upgrade : Master Crafted Prows: All Line Ships are immune to frontal ramming damage.
Unique Skill : Hold Formation!: While the Flagship is alive, all line ships are immune to mutiny.

Their ships break flimsier or less-well made ships like twigs on their prows, and as long as the admiral is their to direct them, their crack-training and discipline means they wont break to morale. Should make them play more aggressively, but also make the Flagship of your fleet an extremely valuable target, so use with care.

Battlefleet Bakka: A subordinate Battlefleet to the mighty Battlefleet Tempestus, responsible for protecting the fortress-port of Bakka which serves as the home base and Anchorage for both these Battlefleets. Famed for its roving Battleship and Battle-cruiser Squadrons, they are fervent followers of the Big-Gun Lobby, which states that carriers have no place in the Imperial Navy.

Unique Upgrade : Super-Charged Macro Ordnance: If Lock On is active, increase Macro weapons gain +50% damage and gain +2.5K range.
Unique Skill : Heavy-Calibre Point Defence Turrets: All enemy ships within 4.5K of a Line ship suffer 1 damage per second (ignoring Armour) if their shields/holofields are down.

All about those Big-Gun Capital Ship. Wants you to use Lock On for more range and killing power, and can damage stuff in turret range if they don't have shields. No filthy and useless Carriers here!

Battlefleet Bastion: A huge collection of fleets which are on permanent Alert in and around the Solar Segmentum, referred to as 'Bastion Fleets'. Their job is smash any fool that dares to try crossing into the heartlands of the Imperium, and they've been doing it for a very long time. They're a fan of Grand Cruisers and Battle Cruisers.

Unique Upgrade: Old Guard: All line ships gain +10/+10/+10 armour.
Unique Skill: Veteran Crews: All line ships have +10 Troop Value.

Meant to be much tougher than your average IN ships, allows them to just survive that much more.

Battlefleet Armageddon: This Battlefleet Loooves lances, since they fight primarily Orks and the range+AP ability of lances is an excellent tool for fighting one of the most active Ork vs Imperial war-zones in the entire galaxy.

Unique Upgrade : Advanced Power Coils: If Lock On is active, Increase Lance damage on all Line Ships by 100%.
Unique Skill : Mark your targets!: Allows your Flagship to Mark an identified ship, revealing it for 30 seconds. Increase Crit Chance on that target by 50% (60 second cool-down).

Imperial Lance builds anyone? Give the Apocalypse some love.

Battlefleet Koronos: A heavy patrol fleet responsible for a huge area of space near the Halo Stars. They have the second best escort fleet in the Imperium (behind Battlefleet Calixis, which isn't represented in this game) and have an unusually large number of Nova Cannons. Preferring to dispatch foes before they ever get to fire back with massed Void Artillery.

Unique Upgrade : Nova Cannon Stock-piles: +1 Charge for all Nova Cannons.
Unique Skill : Improved Auxiliary Crew Training: Increase detection range on all Escorts by +4.5K, escorts have +1 troop value.

Escorts better at seeing things and surviving, and an additional shot for all your Nova Cannons. Classic 1-2 combo.

The Raven guard could have the ability to give all your strike cruisers the silent running stance. It is already in the campaign for all space marines.

White scars should actually get an in-depth upgrade that strips much of the armor on their ships in favor of better manuverability. Whenever they can, they most of the time remove excess armor from all their vehicles in favor of manuverability and speed.
That would be quite problematic, though, as no factions as of yet sport any tradeoff upgrades that would weaken some parts of their ships in favor of others.

Necrons need some Subfaction abilities, and correct color schemes at that. I mean they already exist in lore and TT, like Mephrit's sun guns, so why aren’t they in?

So can someone from gamedev stuff reply us? I hope we got this features, cz we need more differences in sub-factions.

Thanks for the feedback everyone! I've passed it on to the team.