It was decided for simplicity as far as I remember. By UI designers. Do you need a graphical user interface to be able to configure which folder shall be displayed and which not? Will "hacker" approach (an ability to set the list of folders which shall not be synced via gconftool-2 command-line tool) satisfy you?
Could you explain it in a little bit more detail? Can't get you here.
Blame mail client, pls. MfE uses system-wide mail client (modest) and it is implemented in this a way..
... Yep. Missed feature.
... Yep. The ideas of UI guys was - if you have more than 1 notification, than it is impossible to detect what email shall be opened. Instead, folder view is shown and you can select whatever you wish.
Accept/decline/tentative functionality is not implemented.