The difference is in the Xbox 360 portal's internals. The PS3 and Wii/Wii U are the exact same portal. The 3DS, while smaller and wireless, does come with a separate USB cord which can be used with the PS3 and Wii's too. Just something about the 360 required Activision to construct our model differently. All portals are compatible with the PC and can be used with Skylander Universe.
Be prepared, the upcoming Skylanders Swap Force comes with an all new portal.