Don't forget the first game, which would be pivotal to your success.

BBS (not released) --> KHI --> CoM --> 179 --> KHII

As for Re:CoM (PS2) and CoM (GBA), there's virtually no difference between the two. However, if you want the rather insignificant three extra seconds of plot footage, play the PS2 version.

btw, the original GBA game does not have the "Re:" tag on it.