Best game on Kongregate and only 3.8 average score? Must be the dumb people voting it down because it's too hard. No wonder why "toss the turtle" is so high rated.
The Mothership should never target anything but the Energy Generator your repair crews are keeping up. The decoy generator should be the most exposed/closest to the Mothershipt and then it's always targeted. 10-15 repair crews and it won't go down.
The enemy are also stupid... which is good for you, you can lure them into attacking a high-HP outpost that's supported by a dozen repair stations while the rest of your fragile base is left alone.
Hint on finishing the last "boss" fight missions on any difficulty level:
Use a upgraded power station placed on the frontline to absorb the death ray, with some a few L3 pulsars right behind to destroy the purple missiles. Have MANY (10-15?) healing stations within range of that Station, but make sure the station is still the "closest" to the monster.
Use max-level missile bases to deal the actual damage, and level-2 power stations to ensure it all doesn't rune out of juice.
No other weapon types, just missiles and pulsars.
You can adapt this strategy and scale it up for the 3 boss final fight.
 "Battalion: Arena"){kind=icon}
 "Cube Colossus"){kind=icon}
 "Knightfall 2"){kind=icon}
 "The Space Game: Missions"){kind=icon}
 "Dinowaurs"){kind=icon}