Eh, in my opinion porting CT to a Sony system wasn't a bad idea, though it certainly had its flaws. Square has been releasing games on all sorts of system these days, so it's pretty hard to judge what'll go where. For instance, Dragon Quest IX was released on the Wii. And I think SE's development of the Crystal Tools game engine has allowed them to develop games for the XBox 360, PS3, possibly the Wii, and even the PC.
If Chrono Cross were to be re-released as a revamped/enhanced remake, then it could very easily be on any of the systems...with the possible exception being the DS. If they're to just release a port, then my guess is it'd go to either the PSP or to the Wii's Virtual Console.