I wonder if the original evil Braniac is out there somewhere? We've had Brainiac 5 on the show for a while, but I don't remember them ever bringing up his original ancestor at all.
I think Brainy himself will take that road to some degree. Now that he's fully connected to the "Big Brain" he would be nearly unstoppable if he turned into a villain, and if a part of his new personality had some as yet unrevealed issue with say...Superman, that could be natural crossover material for the Superman/Lois show.