I'm honestly not sure if the characters I have problems with are really a result of input delay or lack of knowledge. That said, MoS, Predator and Inferno are problems. I know to fuzzy guard Inferno's Demons low then high, and can attempt to react to overhead/low mix ups, but I often get hit even when I block right. That said, this could be a result of me not having a solid read and not reacting in time.
Reversals are a problem too. I can armour through gaps offline and punish unsafe strings and moves, but the delay often means my punishes don't come out as reversals and get blocked (or don't come out at all because I release block too soon to compensate and get hit).
The counter poke game is also a problem. When somebody is mashing a poke, I can block and try to poke back, but I often get hit out of start up. Predator and Ermac are the worst for this, but it is probably a result of underdeveloped reactions.