Among these issues, I may talk about:

  • Impossibility to remove any mail without using trash: if I use backspace or alt + backspace or command + backspace or shift + backspace, etc. shortcuts, the mail is always sent to trash which I have to empty later.
  • Standard signature separators are not supported (I mean “-- ”). When you answer to an email, not only the cursor is positioned at the beginning of the answer and not at the end, but all text after signature separator is kept.
  • “Non standard” IMAP folder names. Instead of using de facto naming scheme standard for mail folders, Apple Mail uses its own names: « Sent Messages » instead of « Sent » for sent mails folder, « Deleted Messages » au lieu de « Trash » for deleted mails, etc. Then, if you connect to the same account aoth another IMAP client, you get many folders for the same usage. You may change default folders for junk, draft, sent and deleted mails with the following method: first choose the folder you want for specific use, then go into “Mailbox” menu, choose “Use This Mailbox For” sub-menu then wanted usage.
  • Impossibility to choose email charset and encoding. If I send mails using plain text format, and they only contain ASCII characters, mail will be send using ASCII charset. If the mail contains diacritics, Euro symbol, etc. it will use Windows-1252 charset, Quoted-Printable encoded. If I want to disable Quoted-Printable because I prefer using MIME, or I prefer to use only ISO-8859-1 or ISO-8859-15 charsets, I can't: Quoted-Printable is automatically when I use characters outside ASCII charset, and charset is to be choose each time I want to send a mail (instead to get a default setting to be modified), and the list is limited: ISO-8859-1, Windows-1252 for occidental languages (no ISO-8859-15 if I want to use euro symbol without using UTF-8 charset). You may set a default charset with the following command defaults write NSPreferredMailCharset "UTF-8", to enter into Terminal, but the real issue is not fixed.
  • Impossibility to definitively accept an auto-signed SSL certificated for secured connections to an SMTP, IMAP or POP3 server. Then, each time you connect, you will be asked if you want to accept the certificate.

To conclude, Apple Mail is not a bad software but it lacks options and have to many issue to be an excellent software.