So in my recent complaining about ESO lore being uninteresting and no one talking about it, I decided to try and delve into some of the interesting aspects. I've been reading and researching.
The explanation for the Soulless one jumped out to me as something interesting:
http://www.uesp.net/wiki/Lore:Chaotic_Creatia:_The_Azure_Plasm
The idea here is that the Soulless One reanimates when he/she dies like a Daedra and that he's able to do this because he/she has no soul, but does have some other "Anuic aspect" which allows the body to maintain its pattern.
There's further speculation that this can only happen when the Mundus is facing an existential threat. The book speculates that it's like a body fighting off infection.
Combine this with dialogue from the Prophet when he gives you your first Skyshard and I think what's really happening here is as follows:
Skyshards are literal pieces of the Moon (Lorkhan's flesh) called down by the "Heart of Nirn" mentioned in the book, in order to provide the Soulless One with a way to stabilize his form on Nirn without a Soul (Lorkhan is lending him a piece of his divinity to replace the lost soul/divine-spark that the Soulless One is missing.)
This doesn't happen in the latter Oblivion Crisis because Lorkhan's Heart is destroyed/released, taking away the Tower Defense of Red Mountain.