Yeah, just after that big emotional high of BBS, it's tough to follow with a game that originally was intended as an episodic story for cell phones. It DID help fill in some questions in the same way Days did (I kinda get annoyed at the way people harp on the plot for Days...)

And yeah, the clones have hearts, and are at least sometimes able to wield Keyblades, even if it's unstable (see: Xion.) It's an interesting question, but I suspect it's mostly just Sora doing his Jesus thing again. XD