I think that Three Houses could do an excellent job with a "unified" route of some kind. A chance to go into depth with TWSITD as antagonists in a way that's lacking in every other route, justification from the Divine Pulse for Byleth making the different choices necessary (rather than just... doing it, for whatever reason, a la Fates and even Radiant Dawn), and a good opportunity to get characters interacting that we don't normally see interact much (one of the reasons I'm excited for Cindered Shadows, honestly, is maybe seeing the Lords interact more than they do in-game).
They also shouldn't make it, specifically because of how bad Revelations was. Three Houses seems to be an attempt to fix Fates' mistakes in storytelling, with multiple routes and fighting people who otherwise could be your allies, and after Revelations that needs to be left to stand on its own, I think. Even though it could be done and done well, and 3H could get away with it in a vacuum, it's not a game released in a vacuum.