The rules state that if the Ancients can't destroy a ship "the dice should be assigned to inlfict as much damage to your ships as possible, the largest possible first"The dreadnought is the larger ship, therefore it takes the damage. You could state it like that, but that would be counter to what is clearly stated in the rules.
What happens when the ancients do 1 damage and they have to chose between your cruiser with one hull and your dreadnought with two hulls. The dreadnought is the biggest ship, but to the cruiser they could do a 50% damage instead of 33% to the dreadnought. Or you could state it like this: they can bring the cruiser closer to destruction then the dreadnought.
Another question:Because two hits cannot destroy either ship, the 6 damages the dreadnought and the 5 damages the cruiser (because it can't hit the dreadnought). If the Cruiser had only one point of hull, both hits would go to the cruiser (because that would destroy it).
What happens when you fight with one ship with a shield and one ship without a shield against the ancients?
Example: you have a cruiser with two hulls and no shields and a dreadnought with two hulls and a gausshield. The ancients roll a 5 and a 6.
The rules governing how Ancient ships assign damage are very simple:
1) If the damage to be done can destroy a ship, a ship is destroyed. Given the choice, the largest ship possible is destroyed.
2) If the damage to be done cannot destroy a ship, assign the damage to the largest ship in the opponent's armada.
3) THERE IS NO RULE #3.