I did a test program to show it is possible to replace the graphics in 2d emulators, though it incurs a speed cost as you have to hash tile data as it's drawn (which is the most effective way to do it). In my emulator (based off DEGA) you could have alpha blended, 32bit RGBA tiles at 32x32 tiles replacing the original 8x8 tiles. I also added a tool to let you change the tiles.
A friend hosted it for me here :-
http://www.ufowave.com/
The pic below shows some of the tiles replaced along with some tiles left how they are (the sprites are unchanged). I'm a coder not really a great artist, so yeah, it doesn't look as hot as it could with someone talented doing the art.
To answer the question, why not have the possibility?