Super Sonic said:
It doesn't matter because they were going to have different levels anyway. So it is not that big a deal.
Possible, but never confirmed.
On the other hand, a very possible reason is that the WiiS2 versions are actually too full for these stages. Rather than remaking the cutscenes for the WiiS2 game with in game graphics, they've actually ported the exact cutscenes from the PS360 game as an FMV. Obviously these will take up a lot of space compared to cutscenes using the ingame graphics, so it wouldn't be hard to believe that there's actually not enough space.
While it's certainly very impressive that they ported all the cutscenes from the PS360 version, they could have remade them on the WiiS2 version using the weaker ingame graphics, meaning there may have been more space for these missing worlds.