I can't find any site that compares the differences between the US and Japanese versions of Crystalis (a much better name in my opinion). So why should I play the Japanese version, other than the "post credit scenes"?
There had been some censorship, some cuts due to space (like name tags), some errors (like Oak instead of Ork), and the intro in particular had been almost entirely made up.
The lines are no longer indented, which gave more space in the windows, so this new translation was able to flesh out the whole lines with nothing cut, and easier-to-read formatting.
And even though the title Crystalis does sound cool, the name God Slayer is actually more appropriate to the theme of the game. It is about the fine line between scientific experimentation and "playing God."
This is one of the things that Crystalis got wrong. They say that "war" is what destroyed the world, but the Japanese script doesn't say war. It says insolence. In other words, scientists had destroyed the world's natural order. THAT was what lead to hideously warped animals and so on, not war.
That's why lightning is striking the city in the intro, not a bomb, like in the American-made GBC remake. The game is about a retaliation of life against science, the god of modern society. When they cast the tower into the heavens, they were able to reconnect with a more "natural" way of life, and this is why they gained new abilities (their psychic powers).
When you take the tower down, you have "slayed a God," of sorts.