In my experience the thing that Mail users have the most problems with (even before the confusion about how IMAP folders are organized compared to Outlook) is how it handles attachments. Or rather how incompatible the default behaviour is with a lot of Outlook clients out there. A couple of preferences that I've found improve things quite a bit are:
defaults write com.apple.com SendWindowsFriendlyAttachments -bool Yes
defaults write com.apple.com AttachAtEnd -bool Yes
It's the second one, disabling inline attachments, that really makes a difference. Now if only there was a way to always display attachments as icons…