When there are more then 1-2 mailboxes it is more convenient to use some kind of "smart folders" like in Thunderbird. So you can read and manipulate messages from **combined** Inbox, Sent, Drafts, Trash folders. It is obvious how to determine Inbox folder for each account. For other folders mail agent should give opportunity for user to specify it. Smart folders should be listed in "Go to folder" dialog. P.S. It is not duplicated by Favorite folders. Reproducible: Always Similar functionality is available at least in Thunderbird and Apple Mail.app.
You could setup search folders which would have pretty much the functionality you want (except that you can't delete from within a search folder)...