NTSC-U and PAL: very similar, I believe NTSC loads slightly quicker but that could be up to specific hardware instance.

PS2 and PS3: PS3 lags a lot less and loads a fair bit quicker, saving over a minute throughout the run.

JP and US: There is a skip in the airplane level that only works on JP, which saves about 30 seconds I believe.

Kei vs. Yumi: The first morph behaves slightly differently, which makes White Monkey slightly faster with Kei. Some monkeys are a member of Yumi's fan club, and so don't move at all when approached. The hot spring level also starts slightly differently depending on character, as the door opens to either the men's or women's changing room. There's a passage between them, and Yumi's path here is slightly quicker.

In a beginners standpoint yumi is faster, making some troublesome monkeys basically free. theres also a difference in ps2 vs ps3 with the fact that lava has weird interaction on ps3 allowing you to walk along it after getting hit once, as compared to ps2 where it keeps hitting you.

What is the plan once the PS3 PSN version inevitably becomes unavailable?

Well, VC and disc were split into subcategories before there were complaints... I see no reason why that couldn't be re-done if there was demand for it.