December 2008 Mothership Update:
The damage to a mothership is based on a minimum of either damage taken by enemy weapons, or a fixed percent. It is 'modified' by the attack power compared to the defence power. ie - a small attack on a large defence, does less damage than equal attack on defence. This modifier has been increased, such that a greatly imbalanced attack(small) versus defence(large) will do even less damage than previously.
Additionally, a large attack, powering through the enemy shields, will damage more enemy mothership weapons than previously.
This update was put in place, since smaller ships could successfully take less damage than larger ones, because of the fixed percent aspect of the battle. This will move the damage closer, when a small ship attacks a large...