So, just got done watching this. American version last night, Japanese version right now. I prefer the American version by a pretty wide margin.
I find the comedic stuff in the Japanese version to fall pretty flat and the American version to have some of the funnier lines and perhaps even more/better unintentional hilarity. The physical comedy in the Japanese version is probably a touch better...the American version feels a bit neutered in that regard.
And the score...I'm sorry but I think Ifukube's score is all wrong at certain times. ALL. WRONG. It doesn't seem to change up based on what's happening on the screen...from the moment Godzilla and King Kong start fighting until when Kong gets struck by lightning the score is the same, whether they are tussling or there's a break in the action, it's all one constant theme. The music itself is not bad, but it doesn't enhance the mood or the action at all.
Sometimes, the score is spectacular: Godzilla vs. the arctic base, the Kong sleep song, and the airlift music are all great and work well with their scenes. Some of the military prepping the traps and things for Godzilla stuff is good too. The rest, I'd prefer to hear the American version's music used.
The pacing in the Japanese version feels kinda off or something to me too...the editing is bizarre. Take the Seahawk sub sequence. It could be argued that the American version lingers a bit too long on it, but IMHO, the Japanese version cuts away at an awkward time. I also prefer how in the American cut he takes time to get to the Arctic base instead of just apparently coming out of the iceberg right on top of the base more or less. This might just be a preference/what I'm used to from 20+ years of the American version before I ever saw the Japanese cut, but it's kinda odd to me how blindingly fast things jump around from Godzilla to Kong in the Japanese version...like the electric fence part, for one specific example. Sometimes this seems to work, as I know one of my gripes with the American version is that there's a fairly lengthy stretch in the middle third or so where Godzilla kinda disappears from the film, but at other times, it just feels like it's not paced as well as it could be.
End of the day, it's a pretty fun movie. The characters are alright, though Sakurai is really the only one who feels fully fleshed out, but at least they are mostly a colorful, fun bunch. But this falls just outside the favorite zone.