Actually, I think the best thing about ePub 3(.1) is the MathML options. It is really very handy when making mathematics and engineering textbooks available for eReaders. PDF just doesn't work, and SVG can be rather annoying, especially if you make a slight mistake. MathML you edit the code. SVG you create a new file to replace the erroneous one. and with SVG, you end up with a LOT of extra files, making your book SO much bigger than is needed.
I think if anything, it would be MathML and options like it that make ePub3 better than ePub2. (also the css language has improved in ePub3, but we can work around that.)
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