Something I noted in our player character's dialogue, as well as the dialogue of our fellow Scions, is that no one except the Alexandrians thinks their soul system is okay. Some even express disgust or claim it's unnatural, which is an extreme reaction and seemingly odd in a story that explored cultural differences and acceptance as a theme. With the plot suggestions from the raid cutscenes, it's clear now if it wasn't before that their soul system has a dark side.

I think what we'll find, though, is that while their methods are problematic for a number of reasons, it has a broader impact on the Lifestream. Think about it: aether is supposed to continuously flow. When it stopped flowing in the Ancients' time, the Final Days occurred. When aether is processed and stored by Alexandria, it is separated from the Lifestream. It does not go back until the souls are expended and even then, I don't think we can be certain that the Arcadion fighters, as an example, aren't completely expending this aether when they transform. The aether they store is "cleansed" and the memories discarded, but how and to where?

The Rift is sometimes described as the space between worlds but it's connected to them via the Lifestream. Where the story might also be heading is towards a story wherein the Lifestream itself is compromised, as Elidibus foreshadows that something is wrong as he is dispersing in the aetherial sea.

Lastly, the chalice or Azem's relic cannot just be a means to travel. We see it used to manipulate two different sections of space and time, for one, and Sphene also uses it to transform. Whatever it is, it's probably related to auracite, like the Heart of Sabik but on a different level altogether.