EPUB was designed with ebooks in mind.
And it handles metadata just fine, as you would discover if you investigated how EPUB works. Notwithstanding that Dublin Core metadata hasn't standardized on many important concepts like what you mentioned.
CSS styles are The Right Way to define a logical layout for specific elements. Use a house style to make all the ebooks use the same underlying methodology.
But hey, if you think you can do better, go right ahead and show us.
