Thankfully we can take immense comfort in the fact that the Ancients will be honoured and remembered moving forward. I know nuance isn't everybody's cup of tea around these parts, though the story isn't written to pass scathing judgement on the Ancients. Emet-Selch was framed clearly as a hero fighting for his people's survival whereas the Warrior of Darkness was very much in the same situation on the opposing team.

As for the Allagans and the Ancients...well, neither civilisation was lacking in redeeming qualities at any rate - much like how you can see elements of Roman architecture and culture present in modern society in the real world, be it through architecture, language or inventions. Certainly, there's individuals and factions who try to cast society's progress backwards by trying to eliminate such things altogether but as we saw in Bozja, just because a particular concept is tied to a subjective 'enemy' it does not mean that such a concept is worthy of discarding completely.