I think it was because the new Apple batteries don't slide into a slot, like the old ones did. Starting with the Clamshell iBooks and the titanium Powerbook G4s, the batteries were just chunks of the bottom of the notebook.
If Apple were to do that on, say, a MacBook, there'd be no room left for the internal components because MacBook batteries are enormous.
If Apple were to release a thick special "gaming" MacBook Pro, thy could possibly cram two batteries in there, but that's hte price we pay for thin, sexy notebooks, I guess.