I do agree with the points above, especially the one about broken hierachy's. However, I think it would be helpful, perhaps as a "workaround", to at least display folder names based on the IMAP hierarchy. What I mean is this:
Since IMAP folders conventionally handle subfolders/parent folders by using a character like / or . in the folder name, I think it would be useful to allow the user to optionally remove the foldername before the delimiter.
e.g. say I have a folder called parent. Then I create a subfolder in parent called child.
Then I set the child folder to sync in aquamail. In the UI that folder shows up as parent.child, which for me is rather annoying. If there cannot be a UI tree for subfolders, I'd rather aquamail simply treat them as any other folder. (which I realize is what's actually happening, it just doesn't appear that way aesthetically. Although this is a matter of taste, I can't imagine I am the only one who would prefer this behavior. Therefore I think it would be quite useful as a configurable option.