ADAM PREBLE  I recently joined Jungle Disk as the resident card-carrying Mac guy and while I believe we've made some great strides with the now-in-beta version 2.0, there is still a lot of room for improvement to make Jungle Disk feel as 'Mac-like' as possible. One of these ways is, as you point out, to provide an app that lives in System Preferences, or the menu bar, rather than the Dock. At the moment we're concentrating on adding features and keeping the application rock solid, but rest assured that we strongly value the Mac experience and will be making more and more improvements in that area.  
(Version 2.0b1)

ADAM PREBLE  @BEIGE - Amazon S3 buckets do not support hierarchies of files in the familiar paradigm of nested folders, but instead are comprised of a collection of objects (flat, if you like), accessed by key. A number of applications out there store files keyed by the full path. While this is very readable, imagine how expensive (time and money) it would be to rename the root folder of all of your music files, given that Amazon S3 does not allow you to rename keys. You would have to delete the entire 'tree' and re-upload it just to rename a folder.

Jungle Disk's bucket format (which is freely available for your perusal - 2.0 format coming soon) allows you to rename that tree, and perform many other operations, in a fraction of the time and money required by using a full path key format.

That said, version 2.0 provides a new Compatibility bucket type which will allow you to use the full path scheme if your application calls for it.

Finally, if you are having trouble with the application please do not hesitate to contact me through MacUpdate, or post on the Jungle Disk forums. We are completely dedicated to making the best product possible.  
(Version 2.0b1)