Update: Now with picture: http://gbatemp.net/threads/the-3ds-3d-screen-looks-bad-in-2d.340847/page-5#post-4811192
Dunno if you have noticed, but if you completly disable the 3D, the pixels on your topscreen look kinda weird. It seems that both topscreens (the top screen actually consists of 2 screens) aren't overlapping themselves properly when 3D is disabled.
So the pixels aren't exactly 1:1, but I guess they are 1,01:1. This is the case with both 3DS and 3DS XL.
That's why I always play games in 3D at the lowest depth, because the pixels then look exactly like the pixels from the bottom screeen, 1:1.
Fix this Nintendo.
Edit: A more detailed explanation from a gamefaqs user:
"They aren't called scanlines or interlacing. Those lines you see are just the gaps, horizontally, between the rows of pixels. The bottom screen has them too, except the bottom screen also has those same gaps, vertically, between columns of pixels (just like any LCD screen does).
The top screen doesn't have gaps between columns of pixels (or more accurately, the gaps are just extremely small) for 3 reasons:
1: The horizontal pixel count is 800, twice as much as you'd have with square pixels. They're naturally squeezed together so tightly that there would be very little space between pixels that are side by side.
2. Since two pixels side-by-side work as a single pixel in 2D mode, if there were a gap between each rectangular "half-pixel" then you'd actually see 800 individual pixels for each row on the top screen in 2D mode as each pixel would visibly be split in half down the middle.
3. But most importantly... IF the pixels had normal sized gaps between them, then they'd produce terrible moiré patterns with the parallax barriers in 3D mode.
In 2D mode, upon close inspection of the top screen you realize you can't count the individual pixels along each row of pixels (at least not with a plain white background) because of the lack of gaps. Instead, each row of pixels looks like a single continuous pixel because there are no visible gaps between the pixels. In 3D mode, they look like square pixels again, but the vertical "gaps" you see between each column of pixels isn't really a gap... it's actually a parallax bar in front of the LCD. But they certainly do look like gaps."
Dunno if you have noticed, but if you completly disable the 3D, the pixels on your topscreen look kinda weird. It seems that both topscreens (the top screen actually consists of 2 screens) aren't overlapping themselves properly when 3D is disabled.
So the pixels aren't exactly 1:1, but I guess they are 1,01:1. This is the case with both 3DS and 3DS XL.
That's why I always play games in 3D at the lowest depth, because the pixels then look exactly like the pixels from the bottom screeen, 1:1.
Fix this Nintendo.
Edit: A more detailed explanation from a gamefaqs user:
"They aren't called scanlines or interlacing. Those lines you see are just the gaps, horizontally, between the rows of pixels. The bottom screen has them too, except the bottom screen also has those same gaps, vertically, between columns of pixels (just like any LCD screen does).
The top screen doesn't have gaps between columns of pixels (or more accurately, the gaps are just extremely small) for 3 reasons:
1: The horizontal pixel count is 800, twice as much as you'd have with square pixels. They're naturally squeezed together so tightly that there would be very little space between pixels that are side by side.
2. Since two pixels side-by-side work as a single pixel in 2D mode, if there were a gap between each rectangular "half-pixel" then you'd actually see 800 individual pixels for each row on the top screen in 2D mode as each pixel would visibly be split in half down the middle.
3. But most importantly... IF the pixels had normal sized gaps between them, then they'd produce terrible moiré patterns with the parallax barriers in 3D mode.
In 2D mode, upon close inspection of the top screen you realize you can't count the individual pixels along each row of pixels (at least not with a plain white background) because of the lack of gaps. Instead, each row of pixels looks like a single continuous pixel because there are no visible gaps between the pixels. In 3D mode, they look like square pixels again, but the vertical "gaps" you see between each column of pixels isn't really a gap... it's actually a parallax bar in front of the LCD. But they certainly do look like gaps."