I’d argue the name Darth Sidious in TLJ and the clone army line in TFA are the only true references to the Prequels. If no one told you who the Jedi voices were you wouldn’t question it. They’re just past Jedi, doesn’t matter who they are, and that includes Obi-Wan. Granted, Anakin does mention bringing balance to the Force, so I guess that’s one for TRoS. Oh and the RotS quote from Palps.
The entire concept of the Sith being a thing at all was only ever established in the prequels, in the OT the Emperor was just this lone guy with Force powers who managed to turn a Jedi to the dark side. Yet the Sith existing is the basis behind Palpatine’s revival and his plans to transfer his spirit to Rey. So I’d definitely mark that down as an important detail from the prequels.