I think we might consider number 2 (has been requested a few times now)
I don't think number 3 is dooable because to do a 1 click directory upload, we'd need a client side program which would be out of the scope of DA. In theory something written in java would work, but probably more work than we'd want to do at this time as it's out of the realm of what we do (our stuff all lives server-side). I will admit though, it would be nice, but that's why we have ftp. It's been around forever and does everything needed.
Number 1 wouldn't be an issue if number 2 was done, so you'd just change the files over first, then delete them. Note that suPhp is a good option to avoid this in the first place, as files would be uploaded as the user, and not apache.
John