I haven't found any big advantages or disadvantages yet. I still haven't even cleared all levels. My first feeling when playing levels like streets and surface is that it's really smooth, could be placebo so dunno. Doors seems to be open fast, at least the "roller-like" on control. Gonna make a comparison or something.
I think there might be something different tho, I gotta try it some more and explore the levels fully. Hopefully I can get hold of another JAP GE somewhere soon, then I could probably lend it to you so you could try it as well. The levels I've played now on JAP is only the recent WR's. The ending I find is a bit smoother then NTSC I think, cause I got more consistent at the glass. Dam I haven't played much on NTSC but it doesn't seem like they are any differences. Could be laggier/smoother on some parts maybe.
The only thing I know for sure is that JAP is like PAL when it comes to music when you start a level. NTSC continues the music after you pressed "start", while JAP and PAL doesn't. Therefor I'm more excited and positive to find new stuff in JAP version because JAP is NTSC. NTSC-J. But this music thingy kinda proves that NTSC->JAP isn't like a direct transfered and translated GoldenEye.