1) What are people's thoughts about Domina Subjugators?
Not good enough for a tier 5 unit. Low cost, so it's useful to keep a few around, but otherwise kinda weak. Their healing is indeed weak, and doesn't stack, but it's the only mobile healing Advent has.
2) For the Rapture ability Vertigo, how do you use the ability manually in an effective fashion?
Just target in the middle of a big cluster of enemy units, and their damage is greatly decreased for the duration. Excellent ability, at level 3 it will more than half the damage that the target deals.
3) Is the Revelation ability Guidance useful at all? Is it an AoE or only single target?
Nope; it's single-target. For most Advent abilities, they're limited by the fact that they don't stack or that they run out of antimatter, in which case guidance offers you nothing.
The only reason to build a Revelation is for Reverie. Don't waste your antimatter on its other abilities.
4) Is there any context (single player or multiplayer) where there is a useful place for Martydom? Does it only damage ships or also enemy structures?
No; doesn't deal enough damage and it has a stacking limit, not even worth researching.
5) Any use for disciples' to use Steal Antimatter?
Very useful; definitely research this if you have disciples. They not only steal enemy antimatter, but also charge up your own units, which is very useful for your capital ships.
6) What are people's thoughts on Ruthlessness?
Sub-par. If you have malice, it's worth researching. Otherwise don't bother.
7) What are people's thoughts regarding the weapon / shield / hull upgrades as opposed to getting more ships of the same type?
It's a matter of balance. The low-level ones are worthwhile due to their low cost. The high level ones are generally only worthwhile for larger fleets. This can also be a good place to boost your fleet's combat power if you don't want to increase your upkeep. I've actually maxed out all the different damage upgrade lines in multiplayer as Advent; plasma is actually very
devastating when fully completed.
Personally I don't touch the bombardment ones ever
Agreed; very little reason to get these.
8) What are people's preferences for bomber : fighter ratio early, mid, late game for either single player or MP? Just curious.
Depends on what the enemy has. Generally people go bomber heavy, and there's a general consensus that the bomber is the better strike craft overall.
9) Any thoughts on how to use flak to best protect your Destras during big end game battles?
Try to get them so that all their weapons ports are firing. Flaks should be in the middle of the battle with enemies on all sides. The Halcyon, however, is the guardian angel of your capital ships and heavies. Use telekinetic push to keep bombers away so you can close the distance with their carriers. It's not uncommon to see an Advent fleet with 4-5 Halcyons if the enemy is very strike-craft heavy.
10) Does Mass transcendence only preserve the intellects of capital ship crew that perished in a gravity well with the Mothership or anywhere on the map (i.e. separated at destruction)?
I think you're talking about resurrection. Mass Transcendance is a technology that causes all capital ships to gain experience until they reach level 4 (effectively a free upgrade to level 4 for new capital ships).
The resurrection ability does not require the mothership to be in the same gravity well as the destroyed capital ship. I've resurrected capital ships that died over 30 minutes ago with a Progenitor that wasn't even built at the time. It's an awesome ability in long drawn-out games, and in the late-game an Advent player should always strive to have multiple Progenitors above level 6 so they never lose access to this ability.