IMO it's time the synchronisation between a local mail account and a POP3 server is redesigned. Currently only new messages are downloaded from the server and deleted on the server according the POP3 settings. This leaves too much room for different messages count between account and server. IMO this isn't anymore state of the art for a first class mailer. Today many if not most of the mailing is done through ADSL (or similar) while the vast majority still uses POP3 accounts.
In the future the message should be synchronized so on both local and remote are the same message. The server shouldn't store locally deleted messages while still keeping any messages stored locally. Of course locally the messages may be distributed into a folder structure while remote they are kept in the inbox and the remote messages don't carry the "have read" tag, etc.
This kind of input message handling allows to use a simple POP3 account to behave rather IMAP-like. All the messages are available on any access system (home PC, laptop, office PC) without handling spam messages on each system etc. Besides this provides a very simple backup facility in case of a local system crash which a first class mailer should provide.
O. Wyss