SNES pxel art relies on the NTSC color space and natural bleeding to make it look as intended.
Here is a comparison I saved. Here's the image in its raw form:
http://thejayzone.com/pics/snes/ff6_bad2.png
Here's what it looks like with an NTSC RGB filter:
http://thejayzone.com/pics/snes/ff6a_scaled2.png
As someone who owns FF6, a SNES, and a 27 inch Sony CRT, the second image looks much closer to reality. The colors are the biggest improvement, for me. The natural blurring/anti-aliasing adds a lot of three dimentionality to the scene as well, in particularly the stones of the castle. The dithering works well in the second shot thanks to the bleeding, but not in the first shot. The highlights on the stones work far better in the second shot as well.
edit: I had an extreme example saved as well:
I know this is a very extreme closeup, but notice how the second shot gives off the illusion of much greater detail and 3 dimentionality. It's incredible to see how the pixel art acts with the CRT display technology to create something quite special.
That's a shame.