Best bet, like with any aspect of the game, is to mix it up. In the above scenario, you have a plethora of options:
jump-in short->cr. short->knee bash
jump-in short->knee bash
jump-in jab->cr. short->knee bash
jump-in jab->roundhouse AHK->walk-in knee bash
jump-in jab->roundhouse AHK->cr. roundhouse (knock-down, sometime dizzy)
jump-in fierce/roundhouse->fierce AHK->crouching roundhouse (knock-down, frequent dizzy, difficult to time following a knee bash->jump in…for me at least)
jump-in jab->fierce AHK->cr. forward->fireball (the fireball will not combo)
jump-in jab->fierce AHK->cr. forward->crescent kick (crescent kick will not combo, and leaves you vulnerable to counter, but good for flash)
…and other, but you get the idea. For stricly finding additional usefullness for the jump-in short, a personall favorite is: jump-in short->cr. short->jab uppercut (3-hit, knock-down).
The “short arc” AHK (aka juice kick) can be performed by executing it very early in a jump. It is easier to do if “video slow down” is being produced, such as when a fireball hits an opponent, or holding jump forward while in move animation (such as a whiffed uppercut) then executing AHK as soon as jump animation begins. Timing is quite tricky.