I like to read Adobe PDFs on my Kindle. (The Kindle versions that use e-ink have the advantage that they can be read in bright sunlight on my lawn). Normally, to read a PDF, I just email it to your Kindle, with a subject line of "convert". The problem is that with scientific articles that have equations and illustrations, the results are often poor. Moreover, even with regular PDFs, I may get headings that somehow end up in the middle of a paragraph, or sentences that suddenly have a fragment of another sentence in the middle of them.
I don't own any Adobe product, (apart from the free embedded reader in the Microsoft Edge browser), but perhaps there are better converters out there. MOBI is very similar to HTML, and so I could save a PDF as HTML in some adobe product, and then send the result via email to my Kindle (with a subject line of convert), and maybe I would get better results.
What is the best approach (apart from complaining to Amazon) on this?
Actually there is no need to convert a PDF to a Kindle file format. Aside from there being no "clean" methodology for this all Kindle devices can render PDFs.
Registered Kindle owner can email a PDF to their Kindle email account (with No conversion) at no cost.
Or, transfer the PDF from the desktop or laptop via a USB cable.
Done both for the Kindle Keyboard, Paper White, first generation Fire tablet & current generation Fire tablet.
For the Fire tablets install Adobe Reader Mobile for viewing the PDFs. More versatile than the native PDF viewer that comes with Kindle and gives you access to the free Files management at Adobe Document Cloud - PDF Services.