I'm probably going to cover a few points that Cykur has already touched on, but I figured what the hell. Why not. If I don't mention the abilitiy, then I'm ok with what changes you put up there.
Kol:
I'm happy with Finest Hour, Flak Burst and the Shield. Flak burst is sufficient as stands, and the shield fits the "Never Gonna Die" mentality of the Kol.
The GRG seems to be in huge debate here. TBH I'm happy with what's up there. You didn't change it too much. If anything, I'd say only change the antimatter costs. This ability cannot be made too powerful. At most this ability should do 1k at lvl 3. You have to remember that if a Dunov actually makes it to level 6, the current Kol becomes near invincible. -75% cost in antimatter raises the power of flak burst AND GRG by 300% so that it does 4X the normal damage. That's power. Anti-cap power and Anti-Strikecraft power.
Sova:
Give it a fix for embargo, but I agree with Cykur here. Sova rushing worked because you could buy your way to level 3 and get Lvl 2 Embargo out early. I'm not sure if it does, but Embargo should steal minerals too. I thought it did, but i'm not entirely sure it still does.
The fighter buff either needs to be AOE as Eadtaes has suggested, OR It needs to give a much more significant boost to the fighters, as your post has suggested. The ability would need to be nerfed if made into an AOE, but as you've suggested I believe you went a little far (Sova Spamming is a tactic that used to work). Make the Armor 2/4/6.
Akkan:
Just give free mines for the Akkan. 1/2/4 is good. You gotta remember this is a HUGE resource boost considering you don't have to go around spending the time to make them.
Dunov:
Cykur has the right idea. EMP needs a bigger firing arc. Having to fire straight forward means you're going to get one shot off heading into the battle head first, and then it'll be annoying to do it again. The ability costs so much to use and really only destroys antimatter, so 360 degree firing arc is appropriate.
Magnetize needs a bug fix. It only stops abilities from being fired in the future. It needs to also stop abilities mid-use.
Marza:
Leave incendiary shells alone. For a passive buff, the ability is quite good. The ability fits the Marza's balance. You can either risk antimatter stores on Radiation bomb AND Raze Planet, or keep all the antimatter for Raze Planet and use the lesser cousin Incendiary shells.
Radiance:
Leave Animosity alone. when you get a Radiance, you're either getting DA and EAA, or you're getting Animsity and EAA. Either way, Animosity is buffed through the third ability. It also aready has a cap limit on the number of ships that must target it (8/16/32). Since it's a battleship with a lot of armor (most of any Advent Cap, just as much if not more than a Kol with the level 3 ability actually), this ship is already equipped to take punishment. Between repair bays, shield regen, EAA, and the fact that the ship is tough already, I say leave animosity alone.
Halcyon:
Adept Drone Anima. Either make it an area of effect (which probably doesn't make as much sense here as with a Sova, so really I'm just putting the option out there, it's not my preferred option), or go with what you have.
Mothership:
Since the other races colonize abilities are being buffed, I don't see the need to nerf this ability. Cykur nailed it on the head. This bonus is both a blessing and a curse. You get cheap upgrades, but you must buy them in a short time span to take advantage of them, meaning if you want planet health/logistics slots/tactical slots, you must buy them when you get the planet, which means Advent players must spend money at a time that may be less than convenient (TEC and Vasari needn't worry about this, they can buy whenever they want).
I miss the olden days of Malice having a HUGE AOE rather than the current target cap they put on it (8/16/32). It's not useless by any means. It's just...not as useful as before. Just reminiscing.
Just leave Shield Regen Alone. The ability is the ultimate "passive" abilitiy in my mind. Not passive as in costs no antimatter. Passive as in passive aggressive. This ability is easy to counter (Ion bolt anyone?), and Vasari can just bypass shields altogether, so I say leave it.
Rapture:
I actually think Vengeance is still too weak (largely because of the target cap limit on Animosity), but the other abilities on this cap are good enough that this doesn't bother me.
Revelation:
I'm not sure how good Guidance really is, because the only abilitiy I can think to use this where it'll make a significant difference is with Malice or lvl 6 abilities. HOWEVER with Malice I don't think the ability stacks, so really guidance just makes the cap go through antimatter stores quicker and the enemy feels the effect of Malice for shorter time and to less effect.
For guidance, I really think the ability needs a rework. I don't think I've ever used this tactically to any avail. Reverie is the only ability on this ship I give a damn about until level 6. Personally, I'd like to see it scratched and turned into some sort of seiging ability. An AOE effect bonus like the Halcyon, except for seiging, would be nice. This would fit the Advent balance perfectly.
Call it "Induced Decimation". Allied ships that can seige within the AOE get either a damage bonus (Like on the Rapture), or a lower reload time (Like on the Halcyon). Can't be too powerful. At level three I think it would make everything 25% more effective. That'd be enough.
I think clairvoyance needs to last longer. I'd argue as far as double the time, but then again, maybe leaving it alone is a good option too. I say all of this because the whole point of this ability is to get information about your opponent. Right now I don't bother with it because you don't get to see the gravity well for all that long. Just a little too meh at this point.
I'm a bit slow to suggest upping Provoke Hysteria any further. It's already devastating, and you need to remember a Revelation does 50 damage per volley to planets. The only caps that do more damage by normal seiging are the Desolator (53), and the Marza (57). Most other caps fall into the lower to mid forties, so really, the Revelation does enough as is.
Kortul:
See points below
Skirantra:
Repair cloud should have its heal rate lowered by 50% but have it's duration increased by 50%. This would fit the "SAVE THE FIGHTERS" role much better.
Scramble Bombers: I've alread expressed my opinion here.
Replicate forces: Either make it four copies or make the copies last 33% longer. Either is fine by me.
Evacuator:
Sorry, I disagree on coloinze. Leave the duration alone. Either up the build rate bonus or the # of extra constructors ONLY. Doing both is a bit drastic.
Nano-disassembler: Considering the ship has to be facing its target, I think the ability is fine. Just keep your caps away from it and let your fleet destroy the egg. Really, this ability is only useful as an anti-cap ability. (can kill a frig with one shot sure, but an entire fleet with this ability? nope) If anything, make it -1/-3/-5. Otherwise, the incentive to get the ability is kinda gone.
Marauder:
Change the duration ONLY. Instead of 6/8/10, make it 18/24/30. I just think the proposal you've made will never happen. I say that just because what I'm suggesting is easier to program. What you're proposing would make it so that Vasari would never lose a cap.
You've changed distort gravity a bit much. The only change I'd make is the antimatter cost reduction that you propose. I like that. Makes the ability actually useful.
For subversion, I like the idea of doing damage to the population over time. This is a good incentive for the ability. Just gotta keep it small (like 1 population down every 5 seconds because the ability can stack).
Vulkoras:
PMS needs the bug fix.
Leave the seige platforms alone. Leave disintegration alone too.