I'm still curious to know what makes the Japanese version harder. I know someone here has to have played it. Speak up!
I have played it and beaten it, so I am somewhat familiar with all six levels. It was a long time ago though.
Level 1 doesn't introduce much more difficulty, the boss and sub-bosses are slightly harder with more complex attack patterns.
Level 2 again doesn't change much, only the boss seems to be more active in wanting to kick your ass.
Level 3 I don't really remember too much. I think there might have been more of those annoying purple swimming things., Also, I remember the armored things that shoot homing missiles being a bit tougher to kill.
Level 4 really starts the beatdown. If I remember correctly, it's got two checkpoints and is a bit longer. The attack patterns of the purple rocks gets a lot more clever (at one point, they attack from all directions at once, and quite a few of them too).
Level 5 isn't much different than the US version. The boss is trickier to beat though, he moves around a bit more.
Level 6 is a f*cking NIGHTMARE. There are TWICE as many enemies, and the final bosses are FAR harder to beat...with the exception of the final final boss, who is the same as in the US version (there's no way to make him either easier or harder). It's the first half that's the worst though...the layout is similar to the US version except now you've got these annoying green sperm-things that swim in from the top and the bottom that are far tougher than they look.
And there's no half-level skip trick in Violent Soldier either, so there's no skipping the first half of level 6. You've gotta fight every level honestly.