So I know the real world parallel rationale for Khan was the Joker, as in that they had to use the most recognizable villain*. But what is the rationale for the Borg? Batman writers knew they couldn't top the Joker, so they just picked the villain that could best suit Batman's story arc. I would hope that's what these writers would do, but I'm not sure if they would. Picking the Borg seems somewhat fanboyish.
On top of that, since a villain seems to be a necessity, that would almost have to not be a Borg Queen type because wasn't that one of the big criticisms of First Contact? That the Borg Queen was weakening the concept of the Borg and making it seem very cliche? When the Borg were at their best, they were not characters, they were basically zombies or set pieces, giving them real terror. Giving them a very human face full of many human flaws removed any of that.
*despite all the secrecy and not even marketing it that way.