Agreed. Storm is an energy manipulator, but she may only be able to control certain types of energy, either due to intrinsic limitations on her mutant powers, or to a lack of training and experience in how to manipulate other kinds of energy. You can make a logical argument that she should be able to control other kinds of energy, and I would totally buy everything you said, but Marvel almost never takes mutants' powers to their logical conclusion because it would make them too powerful.
Take Gambit as another example. He literally converts potential energy to kinetic energy on a molecular level, which should allow him to do way more than simply make objects explode. It's control over one of the most fundamental processes of physics. Technically, at his full strength, he has used his powers to heal, fly, travel through time, remake reality, etc. But you will effectively never get to see that in the comics, because it would make the other characters useless, and mean you had to invent ridiculously powerful enemies. It's why they always have to nerf Superman every few years.