You've killed us both

[Kein]

I don't think The Shadow is a guardian. After all, Weyer managed to remove several orbs from their resting places without invoking the shadow.

It is. Weyer was just pretty strong person (spiritually/mentally) and thus was able to hold many Orbs.

I think it is a side effect of someone who is not skilled with the orb trying to use its power. It chased Agrippa when he first activated one, and daniel, but not Alexander, or Weyer.

It chased Agrippa? H, don't remember this one.
Regarding "using Orb's power". When Daniel first time saw it, he has NO idea what is this and how to "use " it. But Alexander knew and he has a plan & knowledge how to use it's power. But in the end, it's Daniel who were being chased by Guardian, not Alexander. Why?
The answer is simple: Orb exist to be used. But only by a person who has enough power to do so. Even an innocent child who touched the Orb can be killed by Shadow just because he is small and weak. It is not a matter of justice or sumtin, it's a "nature/balance force" as Alexander says.

Ending 2: Daniel lets Agrippa through the portal. He still hasn't faced what he has done, the shadow consumes him, and Alexander. Though in the end we hear Agrippa plead to Weyer to save Daniel, so we don't know for sure of daniels fate.

If Shadows kills Daniel HOW Ahrippa 7 Weyer saves him?
No answer.

Ending 3: Daniel places the blame for everything he has done on Alexander, and ruins Alexander's plans. He wants Alexander to pay for what he has made Daniel do. He breaks the portal, and the shadow consumes Alexander. Daniel feels as though he has received justice for what happened at the castle and the shadow retreats.

Alexander used first Orb's power (Agrippa's one) and NO Shadow was haunted him . Why? It supposed to. Now, he uses second Orb and NOW Shadows kills him.
Really? REALLY?
It makes no sense at all.