The Ancients are only one of two cases of sympathetic characters not getting a happy ending and the tragedy of it being completely ignored/handwaved. They're the only group that the story gives the Scions and/or the WOL the option of a happy ending but just saying "Nope. You don't get to do that".

The only other one I can think of is Hingashi, where we're told how monstrously corrupt the shogunate is, but for whom the story takes an uncharacteristic "Overthrowing them would be bad" standpoint, and makes us fight against the rebels instead of with them.