1. Top screen subpixels are RGB not BGR
This is weird. The subpixels on the SP LCD are GBR (green,blue,red). The touch screen on the DS is still GBR, but the TOP screen is RGB.
This really doesn't affect much unless you're playing with subpixel rendered fonts or a high-colordepth engine that takes advantage of subpixels (which I've never seen in any current GB game, but has potential with the DS's faster processor.) If you're a DS developer and want to use subpixels, you'll have an extra layer of processing to use the same assets on both screens.
Here's a small demo you can run to see what I mean. The displayed text that is MUCH clearer on hardware when the subpixel order matches.
Swap the screen that the demo is running in and you'll see a marked difference...
2. The Gamma levels are way brighter on the DS
Load up the same screen on both your SP and your DS. The DS is a lot brighter and more vibrant, which is GREAT from a player's perspective. From a developer's perspective, it means that giving the player the option to change their brightness is even more important.
Hopefully, someone will discover a way to detect at runtime if you're on the DS so you can adjust the gamma automatically.