The wall jump is pretty finicky, it was not designed in an intuitive way. I figured out that first I must press the opposite direction of the wall, and then press the jump button, which is something I really have to think about when I execute it. If I can focus and resist the urge to press both buttons at once, then I can use it without a problem. Fortunately, the only time the move is ever needed is when the little creatures show it to you... and even that part might be skippable. I'm not sure, but I do know, every other area you can reach with it is either optional, or accessing an area before acquiring a necessary item.
I think the main reason why people like Super Metroid is because they like to figure things out for themselves, they want to explore the areas and find the secrets and the passageways and all that. And also simply because some prefer 2D games to 3D. I can understand why someone wouldn't appreciate that, especially in this age where games have a lot more direction.
I don't really remember encountering a lot of these "double upgrade" areas you speak of, but maybe I just didn't go exploring until after I had some good tools. I know of a couple, but these have a missile expansion or two after the first section, so you still get something out of it even if you can't get past the next part.