Can we get choices that really matter and have a effect?

[AnimaAnimus]

I can't help but notice that the people who ask for more player choice in the story are usually the ones who want to side with the villains, no matter how obviously violent, deranged, insane, and/or genocidal they are. It's kind of concerning.

They are only villains because we see things from a very distinct perspective. But the Eorzean city states and the WoL could also be considered villains by looking at it from yet another perspective. We lie, cheat, kill, steal all the time, but we are portrayed as heroic for it because what we do is for the "greater good", but who is to say that looking at the situation from the Garlean pov or the ascian pov or the beast tribe pov or the name-any-other-faction pov, that the story we experience would be completely different.

Would you betray the memories of those who died by killing millions sacrificing them to a "God" to maybe bring back some facet of them, which may or may not actually succeed and may only make things worse?

They did not kill, they were beings willing to give their energies to a force of renewal so that the whole may survive. I think you are confusing the ascians who gave themselves to zodiarc with slaves and prisoners viciously slaughtered in some vain attempt at appeasing a god. Emet clearly states that what they did could not be understood by man because man does not have enough empathy for his fellows and for his planet as their ascian ancestors did. Nor the willingness the see beyond their own fragile ego. And the way the events are portrayed on the forums, he was exactly right.