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Once again, I'm not arguing against ePub. The things I'm saying about TeX is just to get a sense of what's already possible as a way of gauging what reasonable expectations are with regard to ebooks. No one need write a DVI driver for ARM if they provide something analogous with whatever they want to use instead.
I think you misunderstood what I was suggesting about annotations too. The annotations wouldn't go into the PDF, they'd go into the source document (which could be an ePub-like TeX-bundle or whatever). The renderer would make a PDF out of the source and display that. It would only need to have one PDF at a time, so the greater amount of space of a PDF as opposed to a DVI or something else would only apply to the active document, and how likely is that to be very significant? In any case, if current specs aren't there, they will be soon. And again, I'm not really pushing for this. It's just that we're pretty much almost there already, so there's no excuse for not getting something as good for what they're actually selling us.
Writing things graphically only works if you're using common notation, or very sophisticated software the likes of which I haven't seen. My background is in philosophy, not math, and most of the "math" I'm interested is actually logic, including arcane notations from the history of logic. No graphical composition engine is going to know what I'm trying to write out of th ebox, not to mention that I don't have any suitable implements with which to do it. (You really want me to draw on my screen with a mouse?) Introducting a new TeX command to type is trivial. But again, I don't object to MathML--if it becomes standard, the tools will come.
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