The Japanese version only works on first boot, if you reboot the console and try to load it again, you will get an awful framedrop and it won't go no matter what you do. The only thing would be to delete the save for it so that the VC thinks it's a fresh boot, but the issue will continue upon rebooting, save states don't help here neither.
Debatable, RE2 on the GC only has the graphics in its favor, everything else is just vanilla RE2 DualShock on PSX.
It was a straight port of that version, the extras are lackluster at best (EX Battle is just meh).
As an avid RE fan, and being RE2 my favorite out of the series and having played all versions available first hand, I can say the PSX versions don't hold up at all. GC version is there for convenience sake, but it's nowhere near the definitive version of RE2.
I still consider the N64 version superior due to reasons, and "better controls" you mention is the N64 version who has the best controls, it has an option similar to what the RE/Zero Remasters did, so without a doubt the N64 one has the better controls out of the bunch, and the graphics hold up incredibly well. The only thing that suffers here is the background resolution and the audio, but it's nowhere near as distracting.
In any way, if you were to go for a "definitive" version of RE2, the Dreamcast one or PC one would surely be the top tiers, and the N64 one being a close second. GC comes third just for the polish in graphics and sound but has nothing else besides that.