Hi, I've noticed some of your comments in the wiki, and thought I'd reply here rather than alter what you've put (as it reads as an "opinion" piece).
Folders first, then files
This Windows Explorer-style way to sort files (first, display folders in lexicographical order, then files in lexicographical order) should at least be optional.
Have you tried Preferences > Project > Folders On Top (checkbox)?
Working with remote files
Right now, I use CyberDuck + TextMate to edit web pages remotely. Other editors such as BBEdit have allowed the user to edit remote files (accessed via ftp or better sftp) directly with no middle man.