Interesting note, I remember reading in a magazine way back when that Nintendo actually prepared for colourizing the original Gameboy games right from day one. It seems to be true, since even games like Super Mario Land display characters, objects and backgrounds with different palettes when playing on a Gameboy Color. It probably made a lot of sense, because the original Gameboy's lack of a colou display was a big and obvious drawback.
Anyway, I don't think Nintendo really planned for any enhancements to be made from GBA to DS. It would be nice if Nintendo included something (I like the note-taking idea), but I think the backwards compatibility is only there as a bonus feature. At most, I expect to be able to switch the screen that is displaying the game, and maybe stretch the image to fit, the same way the GBA does with Gameboy Colour games.