The Theory of Aether

[Berethos]

But the Crystal of Light isn't a tangible item either, it's embedded into one's being. The Warrior of Light can't pull into their chest and grab the crystal. This would mean that you can expend your own life force in the same way you can the crystals.

Like Kaiser-Ace said, they were once physical crystals, we just don't see them in their physical form much after the level 5 (I think it's that one) MSQ where we pick our first one up, or when we see the corrupted crystal dissolve/dissipate after trouncing the Ascian lackey around level 15 or so.

In fact, I honestly don't remember seeing them in physical form like that again until the scene with Ysale heading into Azys Lla.

[Kaiser-Ace]

The Chief Sylph game us the thunder Crystal that represented Rahmu's power after we clear To-To-Rok.

So if the Sylphs had it the it was physical. But when we see the sigil with the Crystals as we get them (and the completed sigil later) that is the metaphysical manifestation after we assemalated them into The Blessing of Light.

[Jonditaru]

I'm under the impression that the enemies of The Crystal Tower were primarily aether. When legends are believed to be true, and enough aether and crystal is consumed, it makes old legends become deities. But who could have summoned these deities? Was it Xande who summoned Cloud of Darkness through aether, or... was it Cloud of Darkness who summoned Xande?

The Cloud of Darkness is the ruler of the Void. She isn't the same as the primals, where she needs to be summoned like they do. Xande was the one that turned to her for power, specifically to destroy Eorzea.

Final Fantasy villains never die like others, their very life force spreads apart into the air. Where do they go? The Void? The air? Do they become aether?

This is incorrect. Not every enemy, or being for that matter, dissipates into the air when killed. This only happens to Primals. It happens, because the only way for them to exist in the physical realm is through the high concentration of aether from crystals used to summon them. When they are defeated, the aether then breaks up and goes back into the world. This isn't limited to the typical elemental primals; Ifrit, Shiva, Garuda etc. King Moggle Mog was the first example of a being who once was alive, summoned back as a primal. Later we get more, where we see people becoming a vessel for the primals with Iceheart, Archibishop and the knights of the round.

Cloud of Darkness was the only one that didn't die when defeated, and her access to aether could have been when the Warrior of Light broke the tower seals. So is it possible that Cloud of Darkness was the same from Final Fantasy III, and it was all of her minions that were what were summoned? And... could the other final bosses be lying dormant in this Void state too?

I'm not sure what you're asking here. CoD is literally a ruler of the Void in FFXIV. The Void is a different dimension within the game, in which the CoD resides. The whole Crystal Tower storyline was adopted from FFIII and worked into FFXIV. So, to answer part of that question: Yes. CoD is the same from FFIII. Just like everything in Crystal Tower. If you haven't noticed it yet, this game is a huge fan service in the sense that nearly every part of the game's lore and story are bits and pieces from old Final Fantasies. On the topic of Aether, it's another version of FFVII's Lifestream.