Kol
GRG needs a debuff other than speed reduction...something like a penalty to shield mitigation, armor, damage reduction, etc...you have to be careful with your duration, cooldown, and stacking limit though so as not to make the debuff overpowered...
Flak burst is okay though if you want you can toy around with damage over time...that's what I'm trying to get balanced with this ability right now...
Adaptive Forcefield probably would benefit from being passive...this change alone would make the other two kol abilities more useful simply because only two abilities would be competing for antimatter...
Sova
In general, the problem with the Sova is that it doesn't scale well into the late game like the Halcyon and Skirantra do...nevertheless, it is still a fine ship and arguably the best cap in the early game...
Akkan
For balance purposes, this ship is fine...
Dunov
Shield Restore needs a secondary buff that it applies to the target...a bonus to shield mitigation would be nice...you may also consider having shield regen over time in addition to instant shield regen to make it more useful for frigates (though this is a little frivolous)...you can also consider allowing the dunov to restore its own shields
EMP I suppose could have better range/shorter cooldown/lower antimatter cost if you think its necessary, but its probably fine as is...
Magnetize could benefit from affecting more targets (note that the finish condition "targets destroyed" and the max number of affected targets are two very different things) and maybe from a greater range...a lot of people also would like to see this ability be cast on friendly targets though that wouldn't be good for AI usage...
Marza
Radiation bomb and raze planet are fine...
Incendiary shells needs a debuff...something like a small armor penalty or even hull damage...be careful with the stacking limit on this one if you add a debuff...
Radiance
Detonate antimatter is fine...energy absorption is fine though armor is not really an Advent thing, could go for damage reduction...
Animosity needs a secondary debuff...something like DPS or a penalty to accuracy/cooldown/speed...
Cleansing Brilliance needs to do more DPS and preferably in a shorter time period...you can shrink the column width if you think its becomes OP...
Halcyon
Fine as is...
Progenitor
Fine as is...
Rapture
You could consider tweaking the cooldown/AM costs/durations of Vertigo and Vengeance but they are more or less okay...
Revelation
Reverie is fine...
Guidance is pretty bad...I'd consider adding another buff, like AM cost reduction or bombing weapon cooldown reduction...
Clairvoyance needs a secondary effect...maybe making the planet more vulnerable to damage, spawn culture, reveal mines, etc...just something...
Kortul
Fine...
Skirantra
Fine...SB is a little on the strong side but if you are making a balance mod one thing you should consider is tweaking bombers (which inherently puts this ability back in place)
Jarrasul
Fine...
Marauder
Phase Out Hull could use some tweaking...maybe hull damage/heal (may want to reduce the amount of damage/heal)...be careful about making this ability OP though, you may have to increase the AM cost (especially for higher levels)
Subversion needs help...longer duration, easier to use (fire and forget instead of having to target planet), maybe damage over time to planet...be creative...
Warp gravity (or whatever it's called) could use a better range...
Vulkoras
PM swarm could probably benefit from hitting more targets...
Other two abilities are fine...
In general, I'd recommend changing the AI use time for the ultimate abilities from OnlyWhenEnemyFleetWillPrevail to OnlyInCombat...Resurrection could be changed to "OnlyWithNoOrders" (may or may not have an "s" on the end)...
Best of luck to you and your mod!