I now have another guess as to who the killer might be. One phrase gave me a major clue:
This sounds very similar to a part of Giratina's Platinum Pokedex entry: It was banished for its violence.Since the dawn of time this being has obliterated countless planets, reaped infinite souls. It did this by impersonating itself as an Ancient, a being you term as 'Legendary', and killing the Ancients one at a time in order to cause instability in the world
Giratina, the being of antimatter, was violent when Arceus first created it; I'm sure it was feared for wiping out entire cities and civilizations with its power. I think some of the reason it did this was because it questioned the authority of Arceus. Arceus, to counteract Giratina's violent behavior, removed some of Giratina's power, created the Griseous Orb, and weakened its attacking strength, thus making it less a threat to civilization. At the same time, Giratina was given its own world where it was the undisputed master.
Then comes the second part of the Pokedex entry: It silently gazed upon the old world from the Distortion World.
I'm sure Giratina is still very angry about Arceus taking away some of its power, so to get revenge on it, it's killing legendaries, causing disorder in the world, and evening out the odds of it winning.
Of course, I could be completely wrong. Either way, I look forward to the moment when the killer's identity is revealed. Cool that Edward caught Latias, and good job referring back to everything. Now his fainting when Rayquaza shot out of the water makes a lot more sense.
Keep up the good work!