So you stack them on top of each other in landscape mode, using the height of the screen which is the most narrow part of it, making them even smaller to view?
And no, on a 5-inch screen, which is only slightly larger than ONE of the 3DS XL screens, each screen would be half the size that they are on their respective platforms, even when blown up beyond their original resolution. So again, hello squinting, and no, that wouldn't be "fine". It's a huge compromise.
And in side-by-side, it's either a mandated layout you can't change, which people would bitch about, or you have to pick the layout yourself based on preference, which could change on a game-by-game basis and frustrate players.
So again, what you suggest is a jury-rig that has very sub-optimal results. It may not be difficult, but that doesn't mean it works as a solution by default.
The easiest solution would be to put in a second screen again, and the struggling against that just leads to concessions that don't need to be made unless you're desperate to be rid of 2 screens, which Nintendo likely isn't.