The SNES-version of Ys 3 has, unlike the PCEngine version, no voice acting and no animated intro and ending sequence. Also some graphics are slightly different. The rest of the game is pretty much the same, although the re-spawn and attack speed of the enemies feels slightly lower. Since all enemies can only be attacked at a certain level – if you’re too low you won’t damage them at all – you have to grind levels a bit more actively than in the PCE-version.
Overall it’s pretty much the same game, but I prefer this version over the PCE-version, since I liked the graphics and the handling better, even if the differences between the two versions are not very big.