There's a reason for that. Since the original GBA screen had no backlight, and even the later GBA SP wasn't very bright either, game developers used brighter color palletes to compensate. The result is washed out colors when playing in other devices, making the game appearance look unnaturally bright. To show this difference here is the snes version of Super Mario World in the left and the gba version in the right.
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Nintendo probably noted this issue and decided to lower the brightness in the 3DS when in GBA mode. I applaud their effort to do so, since in the DS Lite gba games looks like crap. I tell you though that I have a front-lit GBA SP and I can only think that at least someone must have gone blind by playing it in the dark everyday, since the front-light does a better job putting unnecesarry light directly in your eyes than actually illuminating the screen. I assure you, the GBA image on the 3DS is waaaaaaay better.