I loved how the story turned out. And the Ascians have done their share of winning, and they won multiple times, just in the end, we got our victory. We lost at the end of ARR's patch cycle, so it's not like we always win in this game (though I think ARR's wasn't well done). And we were at a stalemate at the end of Stormblood. So actually, it's nice to have a huge grandiose victory of epic proportions akin to how a classic Final Fantasy game would end, because that's what it felt like, a true Final Fantasy finish. Plus, we have several patches to go and we have loose threads. We have victories and losses to go as is.
Are the Ascians evil? Well, I honestly think SE made the Ascians better villains this time round because they've not given us a textbook Disney kind of "good" and "evil", they're not that effective. I do evil because I am evil *evil cackle*. True villains have depth, they have a motive and it is not in one's nature to simply "do" evil for the sake of it being evil. Even if you believe in moral absolutism, somebody doesn't do "evil" for the sake of doing bad, but because in their mind it is good, it is right, it serves some purpose that is positive to them, even if we find it morally abhorrent or is judged morally abhorrent in an absolutist philosophy. How they've approached it is realistic, if anything.
In his mind Emet-Selch is justified because he doesn't consider people to be alive, but a shade. And thus is justified in how treats life from his perspective. Interestingly, the background to all this reeks very strongly of Plato's allegory of the cave. He had the idea that everything in our world is a shadow cast of a perfect 'form' and thus we exist in an imperfect realm. But if one were to follow Plato's idea, we're all still living, breathing things with our own lives, as shadows of this perfect world, we still exist. The people of all worlds in the FFXIV universe are alive and thus a genocide would be putting an end to all those lives, so one could argue that what the Ascians are doing is bad, very bad.
Whilst they may be reborn into a perfect being, their life is still at an end, there is death, there is still loss, there is still pain and suffering and they would not retain any thought or memory of themselves and it is all taken from them without consent. Imagine believing in reincarnation and justifying murder because they will live on in a new form (possibly a better form if their karma is good)? Or believing in heaven to justify murder because they will move onto eternal paradise? Though in the latter scenario, you'd still be yourself, which is different to here.
We are imperfect and maybe incomplete beings in the game's universe, but we are still beings. I get it creates a philosophical and moral conundrum, but I think the fact it does that is a sign of good writing, especially given the cues to philosophy made it feels intentional.