It actually seems like the Founder is indeed the main antagonist. Idriel tells us something about being unable to die and that "he" (presumably the Founder) is afraid of death. Then, the founder asked the mc what he would do to save his loved ones and if would sacrifice the innocent. This leads me to believe that the founder is imprisoning dead people (or people about to die / anyone really) in Eternum to actually save their lives and make them immortal. He probably sees himself as the hero but the people trapped in Eternum probably view him as the villain.
Idriel's words imply that whoever she's referring to is a selfish individual tho. Assuming that
the "Eternum is the Caribdiverse version of the
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" is true, then him closing Acheron and preventing the dead from passing so he could technically live forever (since he could be dead but he doesn't want to cross over to the other side) would be pretty on-brand for said selfish individual.
I dont think that the founder and Thanatos are connected directly (even though the Founder probably gave him the immortal amulet-thing which makes him unable to die).
Jury's still out whether he gave Wyatt an amulet or not tho (could be one of his lies). We'll see in the future if that's actually the case.
William working together with Thanatos seems unlikely, like it would not fit with the different factions trying to get the gems of doom.
I don't think it's likely either, but unless Wyatt has some way to track down those gems through accurate means then someone must be feeding him intel...and the man isn't exactly the kind who's able to do any intel gathering on his own given his current state and personality.
Then again, the founder tells the mc that the amulet lets them respawn without losing their inventory (have not tested that myself), not actually make them immortal like Thanatos, so my ramblings could also pretty much be bullshit.
You can test it by taking the amulet and getting yourself killed in the Collector whodunit. Orion gets warped to some exit portal and he mentions that his inventory is indeed intact. Same can't be said for his relationship with Nova tho (you lose her path if you get killed in that event).
I think neither the Founder nor William are complete Bad guys, but William is an asshole nonetheless.
See my post above. Founder is likely responsible for the current state of Eternum due to his selfish agenda. Not to mention he's responsible for the creation of the excommunication process and has a hand in using dead souls as NPCs. If that doesn't sound like bad guy behavior to you, then I don't know what to tell you.
EDIT: William is obviously not good but at least on the cliffhanger, he did not seems too hostile. Could be that he is just that sure of himself, but I would have expected him to be loud and angry, not calm and actually trying to provide the mc with useful Information.
William wants to control everything as per Axel's and Alex's words about his character. If he could control Orion, then he would likely try everything to do so, even provide him info or maybe blackmail or threaten him later. I don't think he's the kind of person who would be absolutely hostile to someone unless said someone is useless (like Linus) or uncontrollable to him (like Alex).