Nintendo likes to dim VC things, really couldn't tell you why. Something about photosensitive epilepsy?
I'm 99% sure the afterimage is just the 3ds having a bit of screen blur, and is present on all games VC or not.
EDIT: it's added in. I was 99% wrong
I feel like if there's a way to hack power saving brightness, it could be fixed.
Here's my theory:
Say screen brightness is 100%, but the game is only using 50% of the brightness. Power saving will reduce the backlight to 50%, but stretch the game's levels to 100% brightness in software. Result is that the game looks the same and the backlight can run half as bright. But, if we can get it to stretch the brightness to 100% without reducing the backlight, we turn a perpetually 50% bright game to a 100% bright one.