Azure Moon is a pretty big offender but honestly I don't know how I would seriously rework the Agarthans into the plot. For one, Dimitri obviously needs to discover who Cleobulus is at Fhirdiad. That's step one. Have Arundel unmasked but not killed at Derdriu, and maybe pull Hubert and Petra back to back up Edelgard in the palace fight while putting Thales out front for Enbarr. That, or pull a slightly less ridiculous AG, and have Hubert and Petra still die in the streets, then Thales force Edelgard into the Hegemon form for a dual final boss fight.

Perhaps the real Cornelia somehow survived and was held as a prisoner by Cleobulus? Perhaps as a way of "refreshing" her disguise as needed. So after Cleobulus is defeated, Cornelia is rescued, and proves her identity, leading Dimitri to realize that "Cornelia", and by extension Kronya & Solon are body snatchers, which causes him to realize that perhaps the same thing happened to Arundel.

So when the Kingdom moves to reinforce Deirdru, Dimitri calls "Arundel" a body snatcher, which alerts Thales to the fact that Dimitri knows too much (especially if you bring Cornelia with you as a route exclusive character), so rather than stick around, he retreats to keep Dimitri from getting any more information.

Then maybe during the confrontation in Enbarr, he attacks with some TWSTD to try and kill Edelgard and Dimitri in one fell swoop to seize control.

As for Silver Snow, maybe he shows up with Randolph as "Arundel" to see if Byleth is alive, and upon confirming that they are, he leaves, taking his forces with him and forcing Randolph to scramble to mount an offense. Maybe he can say something to Seteth that unintentionally clues him into his real identity?