The fact that Meteion could commune with the dead was disturbing. I can't imagine why Hermes would give her the ability to do that, especially as he did not hold the belief that death was "beautiful" as the others did. Despite my hatred of his character, depending on the dialog options you choose, he does express regret and apologizes for his actions. Venat's not sorry for anything and would do it again, and did if you consider she changed nothing after hearing about the future.

I thought for sure the fact that they chose the name Venat for her spoke volumes based on the character of the same name from FFXII, who was only morally grey if you're feeling generous but definitely presented as an antagonist. It's another reason why I think the gaslighting surrounding her character came after the fact and likely due to someone's insistence that Hydaelyn had to be portrayed/viewed favorably.

As far as her being the main antagonist, it's because for all intents and purposes the Final Days was averted. Mankind had passed Hermes' test and were trying to get back to normal. Her belief that they needed to be able to interact with dynamis was only part of the equation. Mankind had failed her test. It was also premeditated. Not only did she know since Elpis that she was responsible for sundering the world, she gathered people to her cause possibly under false pretenses to help her become Hydaelyn as we saw in the Anyder cutscene in ShB. Everything that happened after that point was a result of the sundering, not the Final Days. I'm not saying that eventually the Ancients wouldn't have had to address Meteion, but they had at least 12k years to figure something out and that was with Zodiark at substantially diminished power.