Now that I have my 3DS back from repair, I have been keeping the styrofoam sleeve it came with in between the screen. I find this annoying, and I'd like to just open and close the screen freely without keeping it in there. My original reason for repair was because of the system's bottom screen scratching the top one. Will the problem be fixed, becuase I'm worried that when I start doing this the scratches will come back.
P.S. - I don't like using screen protectors, they just ruin my experience.
Unfortunately, screen protectors are the only option other than keeping the styrofoam piece between the screens. A screen protector could potentially make the touch screen a bit less sensitive.
Also, the problem will probably not be fixed in a future redesign of the 3DS, because it is difficult for the raised borders of the bottom screen to actually come into contact with the top screen even with the current 3DS. You could ask Nintendo about this with their webform.