Yeah, just pause the timing. You could also do a low jump kick if they are just crouching, and if they are blocking you can actually mindgame them a bit by doing an empty crossover and starting a normal as soon as you hit the ground. A lot of the time when players are crouching to avoid your jump punch, they will wait until they block the punch or see the punch come out before they throw the counter attack. When thats the case, sometimes they will hesitate if you just jump over without an attack, thinking that there is something else coming. Take advantage. Also, this is by no means a quick fix. Just another mix up you can throw in there to keep them guessing.
