Eh, as you say it's a YMMV thing, but to me Rhea and Edelgard are on the same level of "villainy", and indeed parallel each other in a lot of ways. Both are tragic characters who are villainous in certain lights and heroic in others. Both had terrible things done to them by TWSitD, both lie about their true goals, both have sympathetic reasons for those goals, and both do some pretty terrible things in service to them. I sympathize more with Rhea ultimately because Edelgard's starting a war of aggression, imperialism, and working with TWSitD (and sharing their agenda when it comes to the "Children of the Goddess") is beyond the pale for me (also there's some disturbing implications to a number of the Crimson Flower endings, which are more pronounced in the original Japanese from what I've heard), but yeah, YMMV.
Basically, though, I think the relative lack of popularity for Byleth/Rhea comes mostly from a combination of a lot of people playing Crimson Flower first and not knowing the other side of the story, that the game makes it a lot more difficult to get to know Rhea as compared to Edelgard, that she's a powerful religious authority figure and that rubs some people the wrong way no matter what, and that the pairing with Byleth is sort of psuedo-incestuous.