So since there will be a some kind of Motherships instead of homeplanet-command-stations - i have the idea how to avoid the situations when one single super-fast super-annoying ship breaking through the defences and end the game by killing the HCS (or just the situations when naive player lost the mothership by keeping it too close to the frontline).
Idea is in making of the super-armored "core" for every mothership! When mothership destroyed this core is being ejected from the exploding ship and stay helpless and immobilised in the open space - there is no power in the galaxy which can destroy this core, but intead of destruction AI can hack this core to open the door and kill the player who sit inside.
How this is working in the game - mothership being exploded, core stay helpless in the space and player have to rebuild the mothership to escape (there can be some kind of "Mothership lvl" and first one is very little, cheap and weak, but at least he can escape from the enemy). When evil AI see the core - he send a very large amount of units to take the control over the sun system, and send a special hacking unit to hack the core. After 10 minutes of hacking - core is exploding and player losing the game. Also every minute of hacking AI gaining AI-progress and getting a big AI-progress buff for destroying the core... If hacking was prevented by the player - AI have to start the hacking from the beginning, so... Since both sides send all their armies to the fight for the core - this combat can lasts very long time.
There can be a different core-hackers and only one of them is destroying the core after hacking, so AI can send multiple hackers to the player's core and hack the core multiple times and only then - destroy it (preferences based on number of players also).
Some of possible "core hackers":
AI-Progress hacker - producing a lot of AI-progress every minute of hacking, after 5 minutes self-destructs.
Fleet command hacker - after 5 minutes of hacking taking the control over the player's fleet (not turrets) for the next 5 minutes.
Defence system hacker - after 5 minutes of hacking taking the control over the player's defences (turrets and fortresses) for the next 10 minutes
Resource hacker - while hacking the core - all the resource-producing buildings is being controlled by the AI (allow him to create a large amount of units), after 10 minutes self-destructs.
Core destroyer hacker - after 10 minutes of hacking player's core is being exploded.
Also there can be some hacking preferences for AI types - one AI is prefer to chase the mothership and hack the core by AI-progress hacker, another one will try to destroy the core as soon as possible...
