I've been doing a good amount of reading of the lore, and working through finding it all in-game myself - you're welcome to eat my post alive for all you lore buffs that find anything wrong with it.
Metaphysical vs. Physical:
Energy/Power/Magic/Etc
My own opinion is that there is a power in our exile's world that is neither bad nor good innately. It is but a neutral power. This power is referenced several times within the lore as "power" "energy" and "magic". Based on events this power can be used for good or bad.
PoE pulls heavily off the Final Fantasy series, and if you remember the gem support system in FFVII that it's tailored to, you'll remember that of the Life Stream - the planet's energy. The materia used in the game was nothing more than a condensed, harnessed version of that energy.
In comparison with PoE's own "materia system" I do not feel that this is condensed, but that the gems mearely act as a conduit for this energy.
My conclusion came from that of the Allflame. An energy that Fairgraves mentions has only being able to be harnessed in pure-silver. One that gave off a warmth to any surrounding it, and that needed a sacrifice to come to full power.
These points are critical, as Merveil's voice powered by the gem-encrusted necklace that she wore also gave off this warmth to anyone that listened. Allflame is described as a pure energy that was encased in the silver lantern. I find it quite obvious that the same could be said for the gemstones. Merely a conduit of the energy and that energy's harnesser.
Thus the gemstones aren't necessarily the source of the power, but that which it holds is. The metaphysical portion of the gemstone, not the physical gem itself.
To further support this metaphysical version of the power in more of a physical sense - geography may be able to answer some questions as well. There were a lot of occassions where sailors crashed on the shores of Wraeclast - mostly due to Siren's/Merveil herself. In each instance of these reports in the lore it's stated that they had been travelling for months. With this in mind, and the types of wooden ships that were used we could conjure up the notion that Wraeclast may act much like a Hawaii of sorts.
Wraeclast, mentioned in the lore as a "Impenitrable Fortress" and with rocky cliffs would suggest that the whole island is quite rocky and high in nature (Ledges). While you have the shores, even these are sprinkled with craggy rock. Now, taking what we know of geography and with this sort of landmass it's possible that Wraeclast lies on a fault line. In which the top layer of our exile's earth has pushed together to create a landmass - this landmass being closer to the inner rings of the earth moreso than most places. If this energy were to be the planet's power, there's no better place than Wraeclast for it to be accessible to human touch. The same was found in FF7 with the Mako Springs in Mideel. Which may explain why it's so rich with this power.
Also, it's mentioned in the Witches opening that she harnessed Flame, Shadow, Frost and Disease prior to even coming to Wraeclast. Are these gemstones all over Oriath as well or is it that pure energy that she was able to harness without the use of a conduit?
Dreams/Nightmares and Context
While dreams and nightmares(especially nightmares) has seen it's way more and more into the lore there are some issues I see with this:
In what context are they being derived from - "I had a horrible nightmare last night while I was sleeping" "Traffic was a nightmare on my trip home from work". Often times when speaking of specific creatures the NPCs and characters use the word nightmare - but I would have to assume that they're meaning a hellish event or being and not an actual nightmare.
Where dreams/nightmares/visions come into play is that of forseeing the future, or the exile's being plagued with them. The Scion states that she's had nightmares since she was born. The Templar mentions his nightmares becoming truth. Yeena has visions and dreams of things to come.
Perhaps this is the energy. But is this a cause of the energy or an effect?
Prodigies
Reading through the backstories of the exiles, all of them seem to be quite popular and almost prodigies of what they do. Having an innate ability for whatever it is that they've specialized in. The Scion for example explains that she's felt a power all of her life - along with the nightmares. Nessa, being a prominent person prior to her life on Wraeclast seems to know of the names and actions of each of the exiles in their Oriath life when they first get to Wraeclast.
The question I pose from this is, are there those individuals that are more susceptable to using the energy and are also more resistant to it. As all the miscreations found in Wraeclast are those that have used or have been made to use this energy and have had their minds twisted. Are they like Jedi with the force? (haha).
With this, were they pulled to Wraeclast for a specific purpose due to this ability. The templar mentions that he felt as though it was God's will that he was exiled to Wraeclast to perform a greater good.
Light Vs. Dark
Ultimately, my conclusion ends up here. This is a story of Light vs Dark. With an energy source that's being used to wage this war. A war amongst gods, and humans and other creatures as those gods tools. It is said that the Rhoa was created by a child god - which would give evidence (whether faith based or an actual physical child god) that there are multiple gods. The templar believes in the "God of light".
It is mentioned countless times in the lore that "dark" is twisting everything. Zombies - "a dark corruption is represented in controlling them"
"A karui nation thousands strong and still they failed to unravel the nature of
the black spirit. What hope have I?"
Ness mentions the witches power as "black arts"
This is a battle against gods....exiles as tools...Light vs Dark - with an energy to help us wage it.
