I've thought long about this.  I think the solution is to make caps counter caps (in other words, bomber and lrm damage against caps should be severely nerfed).  That way caps are around to support the fleet, and if you want to counter a cap, you build the proper counter cap.  Of course, this would probably require rebalancing caps so as to make caps actually counter other caps, but....

There is a very very very fine line if you raise Mitigation. If you cross it, those ships will never die.

Honestly if you reworked the starting stats for Caps, that would give you the bang for your buck. In our mod we gave roughly ~50% HP, sheilds, and Armor boost. They still go pop. But they last much longer. We also gave Battleships ~60% HP, Shields, and Armor boost plus a ~10-15% Damage Increase.

And on top of all that I personaly have increase the ammount of target they can target. For example the Kol can now shoot 3 targest with its side autocannons. Gives the Battleships awesome coverage against the horde of frigates without increasing the base DPS. So they dont destroy other Caps or larger targets faster.

Anyhow, I think if you want to buff Caps in gerneral stats are the easiest and safest way to go. Trying to justifly their low survivablitly by buffing their abilites over and over is a vicious circle. IMHO of course.

Lessee here...

NO-TOUCHYS (i.e., I have no opinion on):

• Jam Weapons
• Shield Restore
• Phase Out Hull
• Adaptive Forcefield

Now, with that said, my opinions:

Animosity:  I like the code-changing idea.  Doesn't sound difficult, and works well.
Gauss Rail Gun:  Y'know, I only just realized how oxymoronic this ability is (see the wiki articles for differences in the Gauss Gun (aka, a Coilgun) and an actual Railgun for details).  But, back on topic, GRG should slow the target, disable abilities, and reduce armor and mitigation as well.  Basically, Fix D.
Subversion:  Here's an idea that just might work.  Since Subversion actually messes with the planet's infrastructure, as described in the lore, it ought to do some more aside from just hampering structure and ship build times.  What if, in addition, it temporarily lowered the hull ratings of ships and structures in the gravity well?  The justification being that since the Vasari are actively tampering with the ships/buildings, the slipshod craftsmanship has left them more vulnerable as a result.  Alternatively, it could give an "All Trade at this planet is stopped"-buff, as another suggestion.
Phase Missile Swarm:  Not much to say here.  They need to operate like phase missiles (%shield bypass), for one thing, and more damage that affects a larger number of targets.
Guidance:  Alright, so we're burning through our AM a bit faster because the cooldown's reduced.  Wouldn't it make sense if Guidance also added a small AM Regen buff, as well?  It'd make this not quite as non-sensical as it is now.
Magnetize:  I like the "Target Own Ships" idea.  Sounds like that would do it.
Colonize (Jarrasul Evacuator):  I submitted the idea in the "Four Abilities that need help" topic (see post here) that something the Jarrasul could do is give a small %Population Bonus for some time.  It'd need testing to see what all would be acceptable w/out being OP, of course.
Targeting Uplink:  DPS buff sounds good, personally.
Incendiary Shells:  So, stacking is out of the question, it seems.  But doesn't it only apply with the Autocannons, anyway?  Well, in any case, a different idea.  If the target dies while IS is applied to them, it should cause AOE damage to other ships - considering how many combustibles have to be on the ship by the time it goes "boom," it'd seem reasonable to me that some of that nastiness would be flung at enemies as well.
Malice:  This used to be killer in combination with Cleansing Brilliance.  Nowadays, though, its effectiveness has been hampered.  I like the targets affected and propogation buffs, personally.

Another one that I'd like to submit, personally:

Repair Cloud:  This ability was talked about in the past, but it seems to have been forgotten.  One idea someone put forth (can't remember who, sorry) was that it repairs based on the targets affected.  I.e., Frigates are healed more than fighters, Cruisers more than frigates, etc.

My 3.5 cents.

Then caps cannot support the fleet, and in fact don't support the fleet, so people should stop repeating this old chestnut.  The role of caps is therefore colonizing and bombing planets.  Period.  Thanks for clearing this up.

But what makes caps stand out from other ships is their abilities.  If you ignore those, they are just big, expensive frigates.  How boring.

I'm not entirely sure what to do with Animosity, and don't bother with Advent anyways, so I have no comments.

For GRG, the idea of adding several debuffs sounds fine, and so does armor-breaking. However, I do think that simply making GRG do direct hull-damage would be the best course of action. So removing the speed debuff and reducing damage to 250/500/750 would be appropriate in this case. Then at least the Kol becomes a nice cap-killer and complemnts TEC's simple abilities.

Subversion is a lot more difficult to balance. I've stated this before, but Subversion could be buffed by reducing antimatter, hull, and shield restoration rates, and inceasing cooldowns for abilities, for all orbital strutures (And Starbases) in the affected planet's GW. Restoration rates can decrease by 25/50/75% and cooldown increases by 50/75/100%. In this way, Subversion is still very situational, but can be extremely effective in dealing with heavily-fortified planets, And it would make sense in-game- the Vasari sabatoges communications between bases on planet and the orbital structures.

Phase Missile Swarm is easy. Make the missiles be affected by phase missile research, and increase the target cap.

Don't know about Guidance, nor to I really care.

Phase Out Hull is fine.

I agree with Darvin with Shield Restore. However, I do think it would be more balanced by increasing migitation by 10/20/30% instead of a flat 90% rate.

Magnetize is another difficult ability. Negating abilities is nice, but Ion Bolt outclasses it everywhere. Increasing the range of SC being magnetized would help somewhat, or increasing weapon cooldowns by 15/30/45% on the affected ship.

Anything is fine with buffing the Egg's Colonize.

Targetting Uplink is fine the way it is.

Adaptive Forcefield should be a passive, but with decreased damage resistance (But retaining phase missile block), as the OP says.

Incendiary Shells could be made stackable, but possibly only to a limited extent? Making the ability stack up to three times doesn't sound overpowered.

Ignoring Malice.

Jam Weapons is fine.

@Swordsalmon- yup, Incendiary Shells can be made to stack a limited number of times. There's actually a line for that in the buffs.

"Wise man once say, 'If Buff you will read, much will you learn'".

Isn't that obvious?  Look a seige frigates; no one builds them because caps do it better.  What happens if caps in general are made more cost-effective than combat frigates?  The main problem is that you can have as many caps as you want in Sins, compared to say Warcraft 3 where you can have a maxiumum of 3.  Caps have cool abilities, gain experience, and double as siege frigates.  If their abilities are buffed to the point where they out DPS a similar cost in frigates, and out-support support cruisers you have a large problem.

If you give all caps major buffs, the cap ship supply needs to become much more expensive and slower to get.

In regards to capitals being UP late game, what is wrong with my passive buff researchable suggestion?  It solves the problem and if high in the tech tree, means you won't access it early game and become OP.

Four Kols would take down any capital more or less instantly later in the game which is not unheard of amount of caps.  Not to mention early engagements where that level 5 Kol could wipe the floor with the enemy cap(s).  It would take around three shots to kill a capital which is certainly not impossible...

I said it would ruin the feel of the game because of common sense...  Let's say that you are standing somewhere wearing body armor, but are being attacked by 200 guys with sniper rifles trained on you.  Let's see who dies first...  The answer is you.  Its the same way with capitals.

Want another example?  Let's look at WWII battleships.  Traditionally, battleships could take three to four direct hits before being sunk.  Let's see how many direct hits Sins capitals take...  Let's just say that it is slightly more than that.  But simply put, if you have hundreds of little red dots on you, you're screwed.

If you buff them to the point where one ship can stand against a hundred smaller ships easily, something is wrong.  That is an issue with this game.  It is so heavily based on frigates that capitals tend to fall by the wayside later because they do not have the ability to actually fight.  They have abilities.

It is for this reason that I suggested my researchable idea...  It would buff standard stats across the board, but most importantly, it would buff passive regeneration...  A lot...  This way capitals are more resilient, but not necessarily harder to crack with special abilities such as CB.

Also, it is capped at 24 I believe...

You seem to think that I'm arguing with you...  No, I'm not...  I'm simply worried about how much it could mess up the game.  That is why I made my suggestion because it is the only thing I can think of that doesn't risk ruining gameplay.  Sure, you could buff starting stats, but that is bad early game.  Sure, you can buff level up stat increases, but that screws up new capitals late game.  For that reason, I am at a loss...

True, you can, but I don't want to see spamming of level six abilities.  Those need to be hard to get so I'm not terribly fond of the exp bonus.  I want ships to earn it, not get it easily...

Not that I'm necessarily against "having to earn it" per say (if people consider this a critical gameplay element), but I'm also not against NOT having to earn it.  "Having to earn it" is a tactical mechanic.  Buying experience late game when funds are available would be a strategic mechanic.  I always favor the game implementing strategic mechanics over tactical mechanics, every day of the week, and twice on sundays.