If you're referring to GCN/PS2 differences:
GCN version is marginally better. The differences are noticeable, yet small.
Visuals: GCN version has slightly more vibrant colors, sharper backgrounds/textures, and clearer definition on objects and effects. Also supports progressive scan output on GCN. Both versions run at 60fps most of the time, while they occasionally cut down to 30fps as soon as an effect like "Slow" is utilized. From my experience with the GCN version, the transition from 60 to 30 is quick and clean, and the game still moves smoothly at 30fps, unlike say Star Wars Rebel Strike. My guess is the GCN version is using the same engine as the PS2 version, which dictates when to run at 60 or 30fps; given what I've seen from VJ1, VJ2 should've had no problem run completely at 60fps, so there seems to be something holding it back.
Audio: GCN version has slightly better clarity. The PS2 version audio sounds noticeably compressed.
Interface: GCN version loads noticeably faster between menu selections.
Control: GCN version controls identical to VJ1 GCN, PS2 version controls like VJ1 PS2.
All other aspects are identical.
This was a combo of info I've gathered on both versions, and my experience with the GCN version. You don't have to take my word for it.