I forget what game i played, and i don't think it was an RTS but they had it so that the fleet reforms when one of your ships get destroyed so the fleet always looked like the smaller ships were surrounding the larger ones. So i know the fleet formation thing can work. I am not sure how hard it would be to implement the idea that you can't shoot through other objects, that might be sorta hard when every ship has to check to see if it can fire before it does.

Implementing line of sight would be an awesome add on if you can manage your fleet formation to block those lines and protect your cap ships with yoru frigates.

But on makign cap ships stronger all they need if more base HP. Mitigation, sheild restoration, armor regeneration, and armor defence should all remain the same. Just have more HP to buffer the damage more.

Example A ship that had 5000 sheild and toke 5 minutes to recharge those sheilds from 0 to full will now take 10 minutes to do the same 10000 sheilds.

You've got the scale wrong I think.  The ships are tiny, and spread out pretty far, in most maps (compare ship size to planet size).  Also, it you allow blocking of fire, you'd have to allow better control of movement in 3D or it would be unfair... and I don't think I want to see the interface to make that happen.

For my part, I'd say more mitigation is best.  A pure HP buff to the capitals has the disadvantage of making repair abilities less useful (it would take longer to heal the ship)... mitigation doesn't share that problem.

FWIW, I too think that high level Cap Ships are too weak (& expensive)!  Kudos to wnmnkh for another insightful observation.

After reading all the suggestions, I think an increase in Hull (or Armor) with each level, a small increase in sheild mitigation with each level, and a reduction in research, level up, and initial cost would each or ALL be appropriate!

Respectfully, Obi 1

PDS would be great as an ability (Point Defense System)

Seeing them coming and being able to stop them are two different things. And it should be noted that shooting down enemy planes will only save a carrier if this is done BEFORE they launch their missiles. If they come in low, and perform a popup manuver, the planes can be only visible over the horizon for a short time. So conventional radar won't pick them up. And then you have a bunch of sea-skimming missiles coming at you. Oh and of course, Harpoons/Exocets are over the horizon weapons, so they can fire them from 70km+away. They use radar late in flight to track a target. Meanwhile the planes that launched them have already turned around to return to base.

And how well do satellites identify fast moving strike bombers at low level over the sea???

The main issue with capitals isn't really the time they live compared to other ships, since they die just as fast. The problem is that for large scale engagements, the time spent acquiring a target is higher than the time it takes to kill said target.

Using completely arbitrary values for my example.
If we assume it takes 2 seconds to target a hostile ship before you can fire (turning and moving). 
Our frigates can take 1000 pointsof damage before going boom, they deal 20 dps each.
Our capship can take 5000 points of damage and deals 100 dps.

If you have 100 dps incoming damage.
The frigates will last 5*1000/100 + 5*2 = 1 minute. during which they will have done ~3000 damage themselves, due to dead ships not dealing any more damage.
The cap ship will last 52 seconds, during which it will have done 5200 damage, so technically a win for the cap ship.

If you have 1000 dps incoming damage.
The frigates will last 15 seconds, doing ~750 damage before dying.
The cap ship will last 7 seconds, doing 700 damage before dying.

This is the main reason why it stops being economic to build cap ships. I think the fix needs to be more "economic" or "utility" based in nature than "give them more hitpoints", since that will make them insanely powerful at lower fleet levels, while still resulting in their near instant destruction for large battles.
Instead I'd suggest one or more of the following:

• Lower the support cost of cap ships
• Reduce the cost of teching command crews. 
• Increase the xp gained (having them reach mid/high levels sooner would make a loss less costly).
• Allow for predefined leveling templates (same goes for carriers), so you don't have to pay attention to all your cap ships constantly, but can just build and send them into the fray. There would still be advantages to microing your caps, but it wouldn't be nearly as required.
• Let capital ships continue to operate x seconds after they are dead, increasing their usefulness even though they die instantly. This extra time doesn't allow for rescues of the dying ship, just gives you x seconds more to use some antimatter and do some damage.
• Give capital ships a death-effect, so sacrificing a highlevel cap-ship becomes a viable tactic.

Again, the entire list is a "pick and choose". If you implemented everything on this list, cap ships would be seriously out of whack, so don't critique it on that assumption.

You mean something like give it an armor type which offers greater reduction vs. most frigates.... That is already in the game i'm afraid. Doesn't seem to have had the desired effect.

Thanks for all the replies, guys.

I think about this whole issue again, and this is my several newly discovered points on this issue.

1) The number of capital ships are always small in the first place. In current system, it is virtually impossible to build a multiple cap ships unless you completely give up your main forces (frigates, cruisers) and effiency.

2) This means that capital ships are very valuable targets all the time, always causing inevitable focus fire on them.

3) Even with shield mitigation and extra HP, these actually only delay what is inevitable.

The crucial point is that the whole game system actually discourage people from building multiple capital ships, the reasons are, again.....

1) Costwise, they are ineffective in terms of DPS, hp, etc.

-> The cost for capital cap research gets insane.

2) Taks too much time to build and level up

-> Mostly it is all bout level up. There is currently no way to make level 6 ships with safety. And we have some racial imbalance here as well (Advent having better access to this)

Now, we need to understand, that capital ships are intended to be supportive role, never be for main force. So devs give them some cool abilities for that. BUT.....

1) Sometimes the abilities of the capital ships are just not worth at all anyway.

2) We already have a bunch of support ships, some of which have just plain better than those of any capital ships available (subverters, observers' spammable repair, guardian's repulse,)

3) There are many ways to halt/disable capital ships from using the abilities, and since the number of capital ships are few, it is just plain easiler than doing same thing with a massive number of subverters.

4) Some of the abilities are hardly 'supportive' role, rather they are for direct assault (i.e. many of TEC's)

In the end the abilities are just not worhful enough in late game.

I think, the idea of making the capital ships as support ships is flawed. And it needs to be changed to making them more direct and more dominiative.

In games like D&D, level increase is to make each player "survivalble", but in sins, leveling up a cap ship does little to make it survive mid to late game, and so I kind'a shrug my shoulders about getting more cap ships in late game.  They do nothing "extra" after lvl 6 anyway, and it seems just as easy to pop a level 6 cap ship, as a lvl 10 one.  When my cap gains a level after 6, I just say to myself "gee, 2 more seconds of life in the next battle".   If Caps are meant to be support ships, then they just have to have more survivability; more hitpoints/shields, not more weapons.

With Entrenchment comming out, if the new "Missle Cruisers" (that do huge amounts of damage to large buildings) could also do huge damage to Cap ships too (who are as big or bigger than most orbital buildings) then that would be a viable counter:  Cap ships could have much higher hitpoints/sheilds at lvl 7-10, but Missle Crisers could still pop/counter them.

really, I believe mitigation is designed for just that. deep down, it is inefficient from a dmg inflicting point of view to focus large amounts of firepower on a single ship or cap ship. it will in time reach a mitigation level of 60%, and as such, for a short while, 60% of your dmg will be wasted (actually, rather 40%, since iirc all ships have a base mitigation of 20%). since its so short, it does not really make a big difference, but if values were a bit different, then that tactic could come to cost you dearly if the opponent instead distributes his damage among your smaller crafts, keeps mitigation low and destroys several in the process.

the end result is or should be the same as you proposed: focus fire is still possible and to a degree viable. it would after all be nonsense to make ships so powerful that even a continued, massed attempt would not bring them down. but it would come at the cost of not doing as much dmg vs other ships. I'd say that if capships survived even pretty heavy assault for some 30 - 40 seconds, I would think twice before commiting so much firepower to taking them out.

lets not forget: a lot of people said they basically don't use them at all, at least not in the later stages of the game, for all the mentioned reasons. and isnt that a waste? 5 units per race wasted and rarely seen, because their cost appartently do not justify their benefits? for me this is a fairly clear indicator that something is wrong.

They should up the mitigation and shield restore rate. Cap ship armor should be 25% more effective at everything. They should deal frigate-crushing damage at least with their frontal weapons. When my Egg arrives in a gravity well I dont want the enemy to go "Fool! Focus on that ship!" I want him to go "CRAP! FOCUS ON THAT SHIP!!"

They should be feared as a mighty force on the battlefield.