I actually have a 1v1 vs Scorpion session coming up (hopefully tonight) to try and figure this out myself. From what I've already worked out, Commando has the roughest time out of all the variations, due to having the shortest range (b2 and knives make Cyber the best, as you can play footsies at the edge of Scorp's slide range, throw knives, etc, and anti air/b2 punish whiffs, etc. Pre patch, Cutthroat was second due to high damage punishes on blocked teleports, etc, but that's arguably different now).
Run cancel Hellfire pressure isn't too bad, as you can parry or armour though gaps quite easily (ball cancel combo opportunity for those who can do them) and punish ground flames with air ball.
Ninjitsu, I think, is best played outside of his F2/slide range, baiting moves and whiff punishing. This might be easier now with 32-pop up, depending on what was blocked. Blocked teleport could be punished with 112-choke pre-patch for 20%, so if you have the meter, a 30% punish could be in order. Short runs into b13-ex knives after a whiff? Run into Command grab, then anti-wake up throw if you have the meter? (This might be a better use of meter after all). 112 can't really be used for pressure against a turtling opponent, so b31 and grabs might be better up close.
As for inferno, good luck. Maybe work in slowly and save your meter for 32 punishes and anti-wake up? Or breakers, which I find I have to use a lot as good infernos like to mix up their low demon/overhead kick into 30%+ combos.
I'll attempt to incorporate what you've found into my game and figure out some good training mode exercises to practice them.
