I kind of agree on this issue.  Being one that does different articles from time to time I have often noticed how certain graphics, especially math printouts can look so great when in say MS Word format.   But after conversion to PDF format you at times have to well over enlarge the text to even read the math.   Regular prints of these suffer the same problem.   In fact, one of the Editors of our own Journal once mentioned to me he was having problems along this line in something I had converted to PDF.   When I sent him the original in MS word he had not problem at all reading it.   I then suggested he enlarge the PDF version by a bit over 200% and agin he could proper read them.
I believe it is the University of Texas that allows upload and displays of files in PDF, Latex, and MS Word formats as well as HTML, etc.   I have often thought that feature would be good on a all the systems in general.   Another feature out there often absent from websites in general is the ability to upload directly PDF files.  Now websites are not archive systems.   But they do enter into the general spread of information worldwide.   Since most Institutes and most researchers tend to use the PDF format, having websites that allow direct upload of PDF files as well as other types of files would be an improvement from the regular hyperlink to another site.
Just a thought on that last point.

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