I have a friend who for the longest time never saw the weapon effects of wave cannons (an update changed it)...he tended to build fleets mostly of enforcers and carriers, playing the game with a fleet that never seemed to shoot anything...

I completely agree with you; this is why I don't use fleets.

what should be the beginning lab setup for advent

if i build 2 harmoney temples at my homeworld, i need to get another planet (preferably 2) to get 3 hostility temples and illuminators...plus i try to save a slot at my homeworld for a trade port later on

ive tried 3 harmonies and no hostility to get the colonization and trade upgrades fast, and ive tried to go three hostility to get illuminators quickly, not sure which is better

ive found that at the 2 hostility level repair bays and defense vessles can be useful but carriers are just too expensive to get so i only research them relatively late in the game

oh and when is a good time to buy weapon/armor/shield upgrades

My general belief on logistics in the early game is that you do not buy a logistics upgrade.  Build two labs on your homeworld, then wait until you've colonized some planets to build more.  Advent is probably going to want to get two of each operational pretty quickly, but aside from that your priorities are based on your position.

Fast trade isn't necessarily bad, but ensure the enemy is a safe distance away.  For fast trade, I'd build two civic labs on my homeworld.  I'd send a colony frigate to the nearest asteroid and my progenitor (definitely lead progen for discount) to the nearest ice/volcanic.  I'd then scuttle my capital shipyard.  I'd build my third civic lab on the ice/volcanic, then set up a string of three trade ports.  Because you've skimped on logistics upgrades, you can afford your trade sooner and get that income rolling.

what is the point of microphasing aura? its supposed to teleport any friendly strike craft within the radius to a more advantageous location, but the enemy can just turn around and keep shooting them...?

so is it a good idea to get microphasing aura on my second skirantra, while reserving the first one for scramble bombers and repair cloud?

when should i usually build a second capital ship? i find that it's difficult to wait for the resources to accumulate while i am trying to colonize, develop planets, and build frigates and structures

Very much so; it's difficult to save up for a second capital ship early on, and it requires some very careful penny-pinching to pull off.  You have to find little scraps of money you can save at every turn, and then push out that capital ship and put it to work immediately.  If you can level it up quickly enough, two capital ships can give you a big advantage in battle, but this is a risky gambit since an enemy who puts that money into economy or fleet can overpower you in the short-term.

Depends on several factors.  Generally assailants have more firepower (those awesome phase missiles) while enforcers have more durability.  If you can keep bombers out of the picture with the Kortul's jam weapons, then enforcers become very good.  Overall, you won't be disappointed with either unit.

Subverters are one of the most awesome units in the game.  They do come very late in the game, and that makes them quite expensive, but they're well worth your time.  As for a precise mix, it really depends on what you're doing.  One is a strictly defensive unit, the other is a strictly offensive unit.  You do want both, but it depends on what kind of flavour you want for your fleet as to which one you prioritize.

Enslaved labour lowers credit cost, optimized construction lowers metal/crystal cost.

This is really only useful if you're trade-spamming and need to buy most of your resources from the black market.  If you're still selling to the black market, don't bother with this tech.

Subverters are quite difficult to counter if they're used well.  Obviously if you can just kill them with strike craft from a distance, or charge them with light frigates and bring them down, that's preferable.  However, a good player will back up his subverters with a balanced fleet.  There simply isn't an easy way to get at them.

Light frigates upgraded to bring down their antimatter reserves can be very helpful, and any defensive support cruisers that can buy you time to bring down the subverters are well worth the effort.  Otherwise, your only real option is to try to keep your fleet spread out so the subverters don't get too many targets inside their area of effect.  This is most challenging for Advent since you want to keep your fleet close together to benefit from a Progenitor/Guardian combo, but for TEC it isn't that hard.

when do you build a third capital ship and what should it be

i used to go halcyon-progenitor-rapture but i read that the halcyon is generally better than the rapture, now im not sure

The Rapture is definitely the best support capital ship in the game (not saying much; the other support-type capital ships suck), and it has some great abilities.  The Progenitor and Halcyon are definitely better overall, but as a third capital ship a Rapture is a great choice. 

I personally think Vertigo is the most underrated ability in the game.  Extremely dangerous if you can level this guy up, since it's going to more than half the damage of the affected enemies.

Darvin3, I've also run into the problem with ships on the empire tree not maintaining the normal order. I found that this was due to activating/deactivating a mod without a restart of sins. The mod I was running was the Equilibrium mod. Hope this helps.

Updated RAting for CS:

1) Skirantra

2) Progenitor

3) Halcyon

4) Kortul

5) Rapture

6)Sova

7) Akkan

8) Jarrasul

9) Radiance

10) Marza

11) Antorak

12) Vulkoras

13) Dunov

14) Revelation

15) Kol