ok "TLD", "Mr. Applegate" et al. the condescending tone is not appreciated and is what annoys the rest of the world with the Mac Fapping apologists.
"Save As" is FAR more efficient than the current Mac Lion workflow and it would not have been hard to leave in. Additionally, it needs to be implemented better in other ways...
My Most Common scenario (among quite a few others):
you are researching online.
you find a .pdf that may (or may not) have useful information.
you click on it and Preview opens the file (saved in Downloads folder)
you read the .pdf and decide that the information IS pertinent.
you want to hit 'save as' in order to rename the file and place it in a folder that makes sense to you (i.e. 'Bosnia' is more useful to me than 'Downloads')
I cannot do this.
I now need to:
1. 'Duplicate' the file
2. wait for the new (redundant) window to arrive
3. Click Save and then navigate from the top level down through as many layers as required to get where I want to Save (HD_Projects_gendered conflict_balkans_post conflict_Bosnia_Rape Trauma Treatment)
4. SAVE the document with a new name
5. go to the previous window and close it without saving
6. Open a Finder window
7. Navigate to the Downloads Folder and DELETE the original file
8... every file I save with Duplicate+Save makes me start at the top of the file tree and drill down to where I want to be. Yuk.
Workarounds:
1'. Open a Finder window for Downloads and another for the Destination Folder leaving them open on my desktop '(and another for each additional possible Destination folder)
2. View the .pdf in Preview and close it without saving
3. Drag and Drop from the [Finder-Downloads] to [Finder-Bosnia]
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MY Preferred User Experience (keyboard only):
1. I select a .pdf in my browser and Preview opens it.
2. I view the .pdf, and possibly make annotations to it.
3. I use [Cmd-Shft-S] to 'Save As' and hit [enter] to save.
(because it remembers the last place I saved TO)
The original is now edited, and through a 'file-move' operation is now in the right location for my needs, there is nothing left in the Downloads folder.
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I understand that the latter is not how 'Save As' works in many applications/OS's but it is how I would prefer to operate.
Right now, I expend about two minutes PER DOCUMENT just saving it.

@
ALTERNATE WORKING FLOW:
I know about 'Export...' which does much of the same thing as 'Save As' but takes you to the folder where the document was opened FROM (which can be useful when saving multiple named versions of the same document) it also does not do a 'File-Move' so that you can avoid leaving a trail of old useless versions here and there.
Using Export saves a little time because I can rename the file and go back later to the Downloads folder and select 'every other file' that has been renamed then drag them to new destinations, but sometimes I have to reopen the .pdf to remind myself of the contents in order to classify them properly.
[note: What? You say "Just put the subject in the filename for easier classification" - sounds good, but then I need to go through all of them individually and keep the filename but lose the 'classification' portion manually. Ugh! ]