Ok, I have to admit you're right. I was under the impression that pdfshuffler's 
behaviour was the standard one, i.e. all or at least most file dialogues filter 
only on the extension and only offer the "all files" option to get other files. 
But I was wrong, the behaviour you expect is indeed the standard one. Also my 
comment on speed was not really fitting: In my case (folder full of PDFs with 
correct extension) it won't make any speed difference, it would only rely on 
the slow detection if the file has no extension.
The only thing that would remain is point 1) from your description but this 
would really be standard behaviour, e.g. eog would list a file with .jpeg 
extension regardless whether it really is an image or not.

To conclude, this issue is an upstream bug, I'll report it in the upstream bug 
tracker. The patch is actually trivial, in the /usr/bin/pdfshuffler file, 
replace the line 
         filter_pdf.add_pattern('*.pdf')
with
         filter_pdf.add_mime_type('application/pdf')
(Note that whitespace is important for python, i.e. you have to have the same 
indentation as before).

Sorry for my negative earlier response, I learned something new today ;)

** Changed in: pdfshuffler (Ubuntu)
       Status: Incomplete => Confirmed

-- 
pdfshuffler does not recognize all PDF files in directory
https://bugs.launchpad.net/bugs/542755
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