In small games, losing your uberpowerful flagship is generally fatal. Here is an idea to help compensate for this a bit.
How about Flagships get a small bonus in weapon fire rate/shield regen rate/repair rate/accuracy? (can explain it away as the crew/officers/engineers being the cream of the crop). If you lose your flagship, the next capital ship you complete is your new flagship.
This will help players come back from losing their flagship if they can get enough time to build a new one.
now, how would that make losing your flagship less fatal. if anything, it would make losing it at the beginning even more dramatic. what it does is that subsequent capships are not quite as strong as the flagship, ergo, if you manage to rebuild one and get it to a certain level, its a bit better.
I agree on your intentions, but the mode you suggest is not good imo.
you could make a dedicated capship killer ship/ structure, but that would probably weaken them too much and maybe take away from the offensive portion of the game.
maybe you could get some powerful defensive weapon that you can only use for as long as you dont have a single capship. that way the "better" player has enough room to expand and eventually overcome this thing, but it doesnt result in an instant death after cs destruction. hmm, no, that sounds too construed, turtling and effectively only drags the defeat out even more.
hehe, yes, an extremely daunting idea: first capship takes longer to construct, but always cost much less, like half or a third. that means destroying it does give a distinctive advantage, but doesnt doom as much as it currently does. don't ask me how to explain it lore-wise. (its basically the equivalent of say, paying only about 200 gold instead of 500 to revive a low lvl fallen hero in wc3)
