For myself, I think this would be extreamly simple to address by simply allowing multiple "profiles" for downloading. When the downloader appears, have a dropdown where you can select the profile. A profile would allow you to define different destinations (based on camera, user/photographer, or whatever other criteria you chose) between profiles. No maker notes (though that would be a nice option), no registry hacking, nothing fancy.
The next extention to this would be to allow multiple destinations per profile. For example, when downloading pictures for my photography, I would like to be able to first place an untouched copy into an archive directory, which I will burn off to DVD; I then want to place a second copy into a working folder where I actually do my editing. I want to be able to set the read-only attribute on the copy that goes into the archival folder; I would want to transform (i.e. rotate) the copy that goes into the working folder, as well as set several IPTC tags.
But, for now, I'd just love to see v. 4.6.0 work.