Unlike the rest of the game, the caps seem to have become more evenly matched, with just a few tweaks needed to achieve balance. Most of these suggestions are boosts to weaker abilities:
Gauss Rail Gun- lower the antimatter cost further, maybe 50?
Heavy Strike Craft- for this to be in line with the Halcyon how about 20/35/50 bonus?
Target Uplink- add a damage bonus 5/10/15?
Magnetize- the max targets seems odd, decrease the target area but infinite targets?
Incendiary Shells- the chance element seems unnecessarily complicated, and the only 'shells' are autocannon not missiles?
Missile Barrage- the ability is silly as it is and the complaints about it are legitimate, no crew could attack infinite targets with missiles, either implement a target maximum or restrict to a smaller area saturated with non-homing missiles- a proper 'barrage'.
Vertigo- expand area affected.
Guidance and Clairvoyance- antimatter cost, and shouldn't the Revelation have at least one passive ability, how about allowing it to spy at no cost, as it is called the 'Revelation'?
Shield Regeneration- nerf this to at most Skirantra levels of healing, 20/30/40. The Skirantra is a dedicated repair/assembly capital, and shouldn't have inferior repair to a colony ship.
Jam Weapons- revert nerf, increase duration.
Microphasing Aura- effect should level more 4/3/2 20/30/40?
Scramble Bombers- to be more nearly equivalent to the other caps you'd need to double the lifetime, especially as it costs antimatter?
Subversion- add a penalty to the planet, trade/refinery and extractors production
Phase Out- why a shield boost/damage if it affects the structure? Move to ship health, perhaps double the boost/penalty on return- then the Marauder is far more of a combat threat to fleeing caps. The Marauder still needs a heavy boost.
Also- why allow the Egg 'heavy' plasma cannons? If 'heavy' weapons does mean +dps, I'd swap these for the ones on the Devastator and Marauder, and allow the Kol and Radiance heavier pulse and plasma weapons as well.
There may be more than one glaring error in my suggestions, but it might also be an improvement to balance the caps as a set in one thread, rather than several separate threads?