Hmm this is still a rather interesting question whether or not the LCD Panels can be swapped, I don't see why not? While there are new features of the N3DS a lot of them sound software based and not hardware. So let's find out...?
Update!
And the verdict is NO they are actually not interchangeable sadly. It seems they are actually different panels and the connector for the 3D part is different as well. Also it's a bit of a pita to remove the LCDs they are adhered to the frame a bit.
The two side by side top and bottom without motherbaords.
The 3DS XL back light and 3D connector (I assume since the other large connector seems to be connected to the panel directly)
And the N3DS connector for the backlight and 3D.
Well that was fun and educational now to throw them back together. Remember if you are going to attempt something, take pictures and share with us
PS: don't follow iFixit with their "prying apart the two halves of the top case." after removing the four screws, the top part actually slides a little bit then it comes right off.