The Genesis version also has much better voice acting.
The "thup-thup-thup-thup" voices of Glames.
I did think that was kinda cool.
edit: crap, I juts realized that the US version of Valis III doesn't quite do this well, since it makes that noise every time an alphabet character is displayed on screen. For the MD version, the Japanese characters come out on screen at a much slower pace, so the thumping noises of each character actually makes it feel like he has a heavier voice. On top of that, the US one just doesn't look right as it also has the mouth on sync with each alphabet, which is way too fast.
Hmm... I can find the US version intro, but not the JP version. Uhwell...