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.