I've made a few posts about this, but rather than hijacking other people's topics, I figured I'd make one myself to share some of my ideas on how to fix a few conflicts and continuity errors caused by all the reboots.
I'm not sure how many people would agree with it, but I thought the best way to go about it is to designate the conflicting interpretations of some characters as new characters. Like post crisis Lex isn't the same person as Earth 1 Lex, but rather his father. So Earth 1 Lex(let's say he's Alexander) can keep most of his original history and then post crisis Lex(maybe he could be Lionel while his father is an immigrant named Alexei if you wanted to include the golden age Lex as a third separate Luthor character) can keep his Unauthorized Biography backstory and take part in all of the post crisis stories he had. And you could even do stories that cover the tension between father and son or even have them team up for different schemes. Businessman Lex brings the business sense and his Machiavellian mind while scientist Lex brings the purely scientific know-how.
With the silver/bronze age style Lex around, he can be the one that introduces the world to Matrix, the protoplasmic lifeform who at some point takes on the Supergirl mantle when the original, Kara Zor-El, goes missing, retires, etc.
I also thought that some other Kents could stand in as the post crisis Kents, maybe Clark's adoptive uncle could be Eben and his aunt would be Sarah. Or, it could be the reverse. Maybe Eben and Sarah were Clark's grandparents and they could fill the role of the elderly Kents who died when Clark was a teenager which had an impact on him in some way, while the more youthful Jonathan and Martha live into Clark's adulthood.
The post crisis Brainiac could instead simply go by his given name, Vril Dox, or his assumed identity Milton Fine, and still have a connection to the classic pre-crisis Brainiac who was his adoptive father. Maybe OG Brainiac is even the one who gives Dox his android body once Milton's body fails.