The only problem that I see is that the games are running in a compressed graphical state. I then did left and right trigger to bring up the menu and yes you can change the resolution of the screen, but what I can't believe is that the resolution of a real NES game exceeds that of the GBA screen resolution.
Well he GBA has a really weird aspect ratio and therefore unusual resolution (240x160 px). Nes games run at 256x240 px. In the horizontal axis, the 16 missing pixels are no issue, because those are "overscan" anyways - they were usually not displayed on CRT TVs at the time and therefore did not contain the game area (if you run Super Mario Bros. 3 in an emulator on your PC, you'll see a blue bar on the left and artifacts on the right side of the screen in that overscan area, for example).
but vertically, we're missing 80 pixels which PocketNES needs to compensate via scaling, compressing the image vertically. PocketNES also has two different scaling options where it cuts of the excess 80 pixels - one mode has the screen fixed and the top and bottom cut of permanently, the other mode tries to follow your sprite and scrolls vertically if necessary.
Either way, the GBAs home console emulation capabilites are impressive but seriously held back by its low resolution screen.