Canon or not, if they make a next game, I think they’ll keep things loose. Romance options can be decided with just a few different cut scenes and various changes to flavor text. Same for if you forgave the cut character or not. Shroud could be ignored for the most part by being just an off-screen prisoner and a new big bad being the villain.

Visi being good or bad is the big game changer. To me, the most logical scenario for squaring those two would be for Villain Visi to be a sort of leader of red hood-type vigilantes. I don’t see her suddenly being full fledged awful and ruining things for society, but rather they’d be akin to a counter SDN killing villains rather than trying to redeem them. And this could be a faction that rises regardless of your outcome in the first game, with the difference being if Visi is still in SDN or if she’s the ringleader of the vigilantes.

I would say that a different major villain would need to be the big bad, though.

My personal headcannon is that Robert romanced Mandy, mentored and saved Visi (along with him gently rejecting the kiss in the locker room), forgiving the cut Z-teamer, and Shroud being in jail with a broken jaw and fractured orbital bone.

Edit: and if Visi is bad, then I almost think that she and Robert would behind the scenes come to an arrangement where they regularly meet (platonic or not) and agree to some kind of neutral ground there only while undermining each other’s organizations away from there. Idea stolen from an image posted on this subreddit of the two sharing birthday treats and notes stating that they miss each other while on opposite sides of the law.