It would be great to extend the story of the following characters:
1) Meredith Stout, as well as the Militech corporation, which is the corporation that supplied Johnny with the nuke to blow up Arasaka tower. Note: in my opinion Johnny is just an angry rocker poser. In the end, he was always a pawn of Arasaka's enemy corporation;
2) Rogue Amendiares and how she survived. Clearly she sold herself out to corporations, becoming the "Queen of Afterlife";
3) The Peralez and everything that involves Mister Blue Eyes. I strongly suspect there are connections to NightCorp;
4) NetWatch and its fight against rogue AIs.
I could be wrong, but if CDPR bets heavily on expansions adding more clarification, we will realize that the main villains, in this case, Arasaka, is not that "bad" after all. In the end, this game doesn't have a super villain corporation, but a villain that goes unnoticed in the game: Alt Cunningham, the one who invented the psychophage.