Can you tell me some cards that aren't included but are needed for a deck? Maybe i can come up with a replacement.
Super energy removal should first check if you have more energy then you need in game. There is an order you can check this. First control the active pokemon. If AIs active pokemon doesn't has enough Energy to attack there is no need for other checks because you don't have enough energy.
If the active pokemon has enough energy check your bench for the amount of pokemon with energy cards. If its zero super energy removal would target AIs active pokemon and it is not worth it. If you have pokemon with energy on your bench check if you have at least one energy on your hand. If you dont you should check if your active pokemon has enough hp to survive next turn. if it has or you have an energy card on your hand there is no problem using super energy removal and choosing the weakest pokemon on the AIs bench. Colorless energy is preferred to pay of course.
You are right that the thoughts need to be done! But not by you alone you know. :D