I'm sorry this is so messy, I typed it in a hurry. Let me know if I missed anything.
According to Claude in one of the japanese commercial trailers the church is hiding something, Seteth refers to (possibly the protagonist) as having "dangerous blood" (more likely than not a reference to Nemesis), and the adoptive father of Ashe, Lord Lonato, is leading a rebellion against the church. You'd think this would be a no brainer right? A church in a JRPG? Of course it's secretly evil right? That's what I thought, but then I started taking a closer look at things and the conflict seems a lot more complex than I thought it was at first.
The Flame Emperor, the man who orchestrated the bandit attack on our three MCs at the beginning of the game, is also working against the Church of Seiros. We don't know the true goals of him OR his Death Knight subordinate who reportedly kidnaps people at night, but we do know that they aren't friendly to the Church of Seiros either. Now if the "good" and "bad" sides of this were unambiguously so then why would the strict but loving adoptive father of Ashe decide to rebel against the same target that our resident homicidal asswagons have in mind? There's no doubt that Lonato has a decent motivation for doing so since an out of nowhere heel turn makes no sense, but if that's the case and the church has done something to warrant people rebelling against them than why are Red Mask and Skeletor doing the same? Only time will tell I guess.
Then we have "Those that slither in the dark" or the "Nightcrawlers" or whatever. What's THEIR deal? Are they working with the Church of Seiros, that's highly doubtful. They look like your typical Fire Emblem dark mage schemers complete with dark clothing and abnormal physical appearances. It's more likely that they're trying to resurrect Nemesis given what we've seen in the japanese commercial trailers of him busting through a wall and pulling apart some chains and I highly doubt they'd resurrect the man that once did battle with Seiros if they were working with the church, but at the same time we also see Byleth doing battle with him out of context with what appears to be an energy arrow shot by Claude in his arm. I doubt Nemesis is pure evil though given his wide eyed shock at Seiros referencing "The Red Canyon", could this be a look of remorse in his eyes? We ALSO see Rhea falling in slow motion in what appears to be the world's best Emmeryn impression, I don't know about you but that looks like a death to me and a dramatic death like that wouldn't be given to a villain now would it?
All of this information and what little context I have to piece it all together leads me to believe that:
The "true" antagonists will be determined by whose house you choose in some way (obviously).
The villains of this game may have more focus placed on their motivations, since the conflict is seemingly more complex this time around.
I don't have a third thing.