I don't think that the writers succeeded at not making Hydaelyn 'evil' because the deliberate genocide of one's own race and inaction in response to avoidable events certainly qualifies as an evil act in the eyes of many.

I daresay a fair few of us are less interested in protecting the virtue of 'mommy' and are more concerned with whether the story being told makes sense and is logical.

The story intends to move on to new things, though hopefully those 'new things' are compelling and the writers manage to avoid some of the same pitfalls that led to a rushed conclusion of many of the game's long running plot threads. I'm not yet convinced that we won't see the Ancients brought up again in the future if need be - simply due to how hard FFXIV goes with attempts at fanservice and because WoW realised its mistake in rapidly burning through many of the story elements that got people invested in the game in the first place.