at the beginning of GC2 the flagship was an important resource being the only ship that can hunt down anomalies until you had the sensor tech to build more
however this ship quickly fell off into obscurity as you got the tech to build bigger, faster, stronger ships; and i would like to see this ship remain important into the late game
so first off id like to see some flavour to the flagship
give each races flagship some ability that makes it more unique from the other flagships
the Iridium might have a trade module that allows the flagship to set up trade routes with other planets but not be "consumed" in the process like in gc 2
the drengin flagship might start with weapons
the terrain flagship might start with extended range or a faster engine
now what happens if it gets destroyed
i think you should be able to build a replacement on 2 conditions
1) you control no other flagship (you cannot trade or capture flagships)
2) it must be built from your races home-world or a shipyard linked to your home-world
now to keep it meaningful throughout the game the easiest way would be to allow the designing of flagships through the shipyard,
if you choose a hull size and select flagship you should be able to start building just like a normal ship but with a bonus of about 10% capacity and have a selection of "flagship only" components