Yes, you can do this. Expand the viewing panel to show local and remote views then sort the local list by file type. It's then just a case of selecting the type of files you want to upload and uploading them.
When I sort by file type it sorts each directory by file type, not the entire site. So I have like 600 directories each with hundereds of files. Its not like I have 10,000 files all in one gigantic directory :(
So is what you're saying still applicable? I'm not sure I understand then.
I have been a long time user of NetLoad (long since out of business) and recently changed over to Site Publisher. This tracks what is on the server in a cache and will quickly upload only the changed files - html and images. Quickly means 2-10 seconds to see what is needed to upload from 3,000 files plus upload time.