1) The primary glitch seems to be that curves in the plot (though not
the plot axes) show up greatly thickened when opened in certain versions
of Illustrator, e.g. with a line thickness of 38 pt. Dashed lines also
show up with greatly lengthened dashes and spaces, e.g. with
(51,51)-point dashing.
2) The problems in any one plot can be fixed by hand editing, i.e., by
selecting the faulty objects and correcting the line widths or dashing
parameters using the appropriate Illustrator tools.
3) The problem has been observed on multiple installations of
Illustrator 11, but seems not to occur in Illustrator 12 or 13 (or
possibly in versions before 11). This occurs independently of whether
the graphic is Exported, Saved as Selection, Printed to PDF on a Mac, or
otherwise extracted from the Mathematica notebook. I do not recall it
happening in Illustrator 11 with Mathematica 5 or earlier.
4) The graphic appears to be fine if the PDF file is opened directly in
Acrobat, Adobe Reader, or Preview (although Preview seems to convert all
text to un-editable outline formats).
5) The problem, whatever it is, goes away if the file is opened in
Acrobat, Saved to Postscript format, and the Postscript file then opened
in Illustrator. The problem is also solved in some cases if the Reduce
File Size in Acrobat is applied to a problem file.
The bottom line of this post is that it does seem to be the case (as I
think someone else reported earlier) that the problem does not occur if
the original graphic is Exported (or Saved?) in EPS format. The
graphics open on a letter size artboard with all graphic elements
apparently OK, and can be saved from there to PDF.