Some thoughts on the villains and villain agencies.
The whole villain schtick is not fully developed yet. High tech weaponry is not as wide-spread as a standard superhero campaign/comic book. Bad guys operate on a more local scale. VIPER cells have finite resources and threaten cities, not nations (except maybe Lichtenstein or some of the smaller microstates, but never Singapore). The mad scientists are aiming to conquer the world in one fell swoop.
I don’t plan on making the villains common criminals, even when they’re robbing a bank. If they’re there in broad daylight, there’s a reason and it usually has to do with picking a fight with a “superhero”. If nasty things happen, they’ll probably happen off-stage and for a specific story reason, never randomly.
Rivalries will happen on both sides. Goodguys can fall, but badguys can be redeemed. There will be cases of mistaken identity.