k2pdfopt is supposed to help with some of these things, but I can't find any clear instructions on how to install the Mac versions.
I don't know if it allows minimal batch conversions, to address the "this pdf cannot be opened due to embedded features not yet supported on Kindle" and "some elements on this page could not be displayed" bugs.
I know the former appears in certain pdfs with security: password encrypted, but not all with security: password encrypted. It's quite unpredictable. My pdf tools sometimes fix this, sometimes don't.
I know the latter appears in some scanned pdfs, removing everything and leaving only blank pages, and some other pdfs, removing images. I guess in the last case it's more of a nuisance than a document-breaker.
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