When you want to do your super or ultra 1 you have to do something called kara-cancelling. Kara means empty, its when you cancel out of the startup frames of an attack, I’m guessing that’s what you are trying to do. If you want to kara super it is meant to be difficult to not land the light punch. Instead, what people often do is forward+medium punch (akuma’s overhead) because of its long startup you can cancel out of it into your super. However this is difficult to do also without landing the attack.
To practice this go into training mode, (assuming your facing right) hold the :f: direction and push the training dummy all the way to the right. Keep holding :f: and press :mp:, now while still holding :f:, press :lp: twice then hold down the :d: direction (now you should be holding :df:) then press :lk: and :hp: at the same time.
DO NOT TRY DOING THIS FAST. Just do the motion. Don’t try and do it fast, keep practicing and as you get faster the super will come out. Sleep on it and the next day you will get closer. This takes practice.
Also look into double tapping, double tap the :lp: to get faster cancels.
As for your gamepad, you either need to GET comfortable by practicing until you get it right (like a combo) or use another input device. Anyone who has used a fightstick knows doing these motions when they first got their fightstick was uncomfortable, but after weeks of practice it becomes natural.