The "Mega Bomberman" version is far worse than the original PCE version (Bomberman '94), in my opinion. The graphics, sounds, and music are all compressed and thus are pretty bad in comparison. You should try the PCE version instead, if you can - actually, the PCE version's graphics are more detailed than those of Super Bomberman 3. You can even buy it on the Wii U and Playstation Network if that's your thing.

Bomberman '94 has its faults, but then, so does Super Bomberman 3. I'm not really sure if one of them is better. I will say that the three final bosses of Bomberman '94 are far more challenging than the two in Super Bomberman 3, so the game is better in that regard for sure.

Personally, I prefer Super Bomberman 3, but that's mainly due to nostalgia and my own preference for the villain characters (and Battle Game maps/characters/items). I think Bomberman '94 holds its own though.