Ok, so this is how I found the FPS code For KH3D. Though for anyone with a powerful enough PC (it seems to run fairly well on my 4670k at 4ghz), there's a 60fps hack for the PS2 version for use in PCSX2. Vita port seems to run at a fairly solid 30fps most of the time.
The best way would probably be the PS3 version.
Though the lighting is slightly better and they added a crouch walk move which was welcome (though this is negated by the controls being worse in other ways). The jungle foliage has significant reductions in both density and draw distance. There are also other issues with Snake Eater 3D besides the horrible framerate too. The GPU in New 3DS did not receive a bump in clock speed like the CPU did. I'm suspicious there's poorly optimized GPU programming causing some of these dips, beyond just the CPU speed. And playing on the New 3DS via homebrew to unlock the extra CPU speed doesn't completely fix this either, cutscenes still constantly drop into the mid teens. But it frequently drops into the low teens and even sometimes single digits. It's locked to 20fps to begin with (the original had occasional performance dips as well but was at least locked at a higher 30). Click to expand.Snake Eater 3D's performance is shockingly horrible.