I have come to the conclusion that Amalthus is actually the most sympathetic villain in the game
**Literally everything up to his death at the hands of Jin is caused by shit that is completely out of control or a botched attempt in fixing the things he fucked up. His life started out (effectively) with his mother being killed by bandits/ whatever bad guys- which caused him to start hating the world. However, despite this, he still lived a "virtuous life", helping the needy and the life, despite his inner thoughts. In one instance, one of the guys he helps turns around and murders an entire family and loots the house, which again is only stopped by Amalthus' intervention. It appears that at this point that he seriously begins to question if the world is as it should be, so he climbs the World Tree to ask the Architect if this the life that was intended. When he got there, he couldn't find the Architect (who later revealed that he refused to speak with him, fully knowing what would happen if Amalthus took the aegis crystals and awakened them).
So with "heaven" basically empty, Amalthus takes the things that he finds there as proof he was there, and then later awakens Malos. Amalthus apparently didn't realize that Malos would be totally colored by his hatred of the world, rather than his good deeds, and Malos then proceeds to act on "hating the world" by attempting to destroy it. Amalthus, knowing he fucked up but not knowing how, then has someone else (Addam) awaken Mythra, who then beats Malos at the cost of destroying several continents.
So Malos gets beat, and Addam returns home to Torna. Amalthus, seeing how destructive the Aegis blades were, resolved to completely destroy Torna, so as to make sure that their world ending power would never be used again. Unfortunately, unbeknowest to Amalthus, Addam actually was first sealing away Mythra in the belly of this giant Torna ship, and he disappeared afterwards, which means that Amalthus, attempting to fix his mistake, instead destroyed an entire continent for nothing. Amalthus at this point decided that based on what he found at the World Tree, no one would ever be permitted to scale it, so as to prevent the destruction of the world.
Over the years it appears that Amalthus began collecting blades and core crystals, and it appeared that his views were changing as well. As his only real contact with the "divine" was through Malos, it appears Amalthus began to arrive at the conclusion that since Malos was born of the "divine", the Architect must also hate the world and want it destroyed. This began to feed Amalthus' delusions of grandeur, and he began more and more to see himself as the chosen of the Architect. To this end, he began collecting blades and "cleansing" them in order to fuel his big dumb superman suit.
However, this wasn't enough to make him become "evil". What really began to tip him over the edge was the arrival of Rex with Pyra. He also realized that Malos had returned, and he desperately wished to correct his mistake once and for all, and find a way to get rid of both Aegis. So he recruited Rex to kill Malos, and ideally find a way to get rid of Mythra/ Pyra before they, in his mind, went the way of Malos. When Rex failed to kill Malos, and Pyra/ Mythra was taken, Amalthus desperately tried to take matters into his own hands using Indol itself and the other titans to kill Malos.
He became even more desperate when he learned that Rex had no intention of killing Jin and Malos, only in stopping them from destroying the world, and that Rex intended to climb the World Tree and meet the Architect.
When Mikael destroyed Indol, Amalthus escaped and sought to stop Torna from ascending the World Tree. To this end, he killed Patroka and Akhos to fuel his machine, and attempted to kill Jin to once and for all prevent anyone from ascending the World Tree. In the final moments of his life, as Jin proceeded to impale and freeze him to death, Amalthus, in a frantic cry, questioned why he was not the Architect's choosen, despite living his entire life by his will. His last words (besides "Mother, I've missed you") were "Father, why won't you answer when I call?"
Amalthus spent his entire life in service to the Architect. He dedicated everything he did to doing what he believed to be the Architect's will, and with all the information he had, he has a pretty good reason for thinking he was right.
tl;dr Amalthus did (almost) nothing wrong**