It is true, even in the epilogue video of cloud in crisis core, it seemed like he had the black uniform on, albiet slightly modified from what zack dressed on him during the nibelhiem escape, but why do you suppose squaresoft(at the time) made cloud wear the blue uniform in all the fMVs, as well as make his field and battle model blue? And instead of messing with the established colors and storyline, they could have very simply made the in game uniform, as well as the final cutscene uniform have more of a blue tint. Now there is also this confusion about what is really the story.
My personal taste for my current playthrough, since I can't change my FMVs, is to at least have the field and battle models with similiar colors, so the transition isn't quite so jarring. To each their own though, that's the awesome thing about mods!