My hot Three Houses Take: The story would have been more interesting without those who slither in the dark.
Think it takes away the confilct? Not really. It’s not like the system doesn’t still heavily rely on crests to be, a very arbitary characteristic that you don’t earn. It’s not even solely about families, as seen with Mikhail and Sylvain. It’s not like the church doesn’t still have a monopoly on power. And however Rhea might talk about Cyril or Cyril about her, her actions and influence had a part in shaping Fodlan’s views about foreign lands. It’s not like the secret society of slitherions invented xenophobia. And it’s not like you need a global conspiracy theory organization for people to do immoral experiments with the end product of obtaining crests. You don’t need that organization to be the only one interested in destroying countries relations with each other (i.e. what happened in Duscur).
Honestly that would clean up Edelgard’s narrative more than it would destroy it. The slitherions didn’t give her a crest, because that would give her and them status. After all, she’s hiding her crest. It’s solely about the power of a crest for them, specifically the power of the sword of the creator one might wield with that crest. And if the experimentation backstory her reason for hating crests, she should hate the slitherions and not the church, where Rhea probably has an incentive to suppress those kinds of activities. But if more people do it, for the sake of status, then that’s just a consequence from the unequal system that the church has heavily pushed (whether it intended to do so in this way or not) for.
You don’t need to make Rhea evil, but focusing on this issue would also stop her from suddenly becoming good. Whether the pre-time skip story was intended to serve as a red herring and make Rhea seem unlikeable or not, she did kind of do horrible things and was implied to be able to do worse. That’s... not really debatable. She did order the mass execution of people who were tricked and framed. And she didn’t do it, because they hurt others. She did it, because they robbed a holy site.
You know the interesting thing about Three Houses set up is that there are a LOT of players right from the start. And they all have their own histories and grudges and views on the current system. How about everything bad that ever happened and continues to happen isn’t directly linked to one group of terrible evildoers? That just makes everything boring.