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There's a lot of negativity for pdfs here (which is understandable), but for those of us who need long and difficult equations, really there's no other formant available besides latex to pdf or postscript. Epub and mobi just don't support complicated equations.
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Actually most people are fine with PDF's. I know I am (except on 6 inch screens). Most of the negativity comes into play when someone wants to turn a PDF into something else. A PDF just doesn't convert well... easily. I doubt it ever will.