Please: A plugin or standalone app that recognizes metadata associated with documents from academic journals. Please.
You could use the program Papers as your “stand alone”; it does what you want excellently, and now has a very basic, but strong, iPhone app for mobile access. The app pulls all of the metadata very successfully from the major online repositories, and renames them consistently according to your instructions.
I use it with DTPO by having an “articles” folder in the Finder, that Papers renames and files all my academic articles to upon importing them into Papers. Then, I have DTPO index/sync (not import) all of those files (and other academic writings not in Papers, like book chapters or books, which are in their own folders) into a Database called “literature”. Lastly, for individual research projects, I again simply index/scan the particular articles I want in that project’s DT database.
If by “recognize”, however, you simply mean that the Info Pane list all of the metadata associated with a PDF, then I also look forward to this feature. However, I don’t think that PDF’s (at this time of writing) embed all of the publishing information; for example, in Papers, my understanding is that the program pulls that info from the journal repository, and stores it in Papers’ own database library.
I appreciate how well Papers does what does and used it concurrently with DTPO and Sente. Between these three apps, beyond the idiosyncracies of individual ‘workflows’, I was simply spending too much time managing file structures, formats, and redundancies without seeing a real benefit to running all three. Using an external word processor adds a forth app to the workflow-not too mention the presence of hard copy materials. Suddenly I was spending more time managing the tools of data management than in research and writing.
My interest is in an application from DTech that would compete for market share with other citation managers (Sente, Endnote, Bookends, etc.).
(You must be right about the difference between metadata which refers to the creation and version histories of the pdf and that which is relevant in the context of academic citation.)
What I would like to see (and purchase), is a DTech app which leverages both DA and DT with a citation manager platform-if only to work within one contextual system instead of three. This is surely something that would be profitable and already has a customer base.
I know I would buy it and use it in a second. Just like I would buy an apple-made 10" netbook in a secon. 
I do think it would be better as a stand-alone that is well-integrated into DT, just like DA. That, or some kind of close association with a particular reference manager (Bookends, Sente, whatever).
I’d certainly buy both too!
Anyhow, I think that better playing together would be more interesting and feasible. Building a reference manager doesn’t look like a simple thing, and it’s a job in itself (look at what the people behind Bookends and Sente are doing). So building that functionality into DT could result into a not-so-good reference manager (that’s what’s happened with Microsoft building its own minimanager into Word).
What would “working together” mean?
First of all, reference managers should be able to seamlesly store attached files in DT, something you now can do by hand… almost.
Second, some kind of interaction should be available, such as creating a reference record starting from a DT stored doc (create the record, attach the file, extract any metadata there might be and insert it in the record, and let me fill in whatever is missing. And being able to download a file in the reference manager (a pdf paper) and having it imported into DT and attached to the record.
Third, there should be an easy way of inserting citations into text in DT, similar to the way Mellel and the managers interact: a shortcut to go to the ref manager, another one to switch back and insert the citation).
The ability to scan documents inside DT doesn’t seem so important to me (I’d do the finishing in Mellel/Pages or even Word, God forbid).
Building this kind of interaction shouldn’t be so difficult, and in any case much easier than building a new reference manager from scratch.
Can’t wait for it.
Hendrix-- what you describe for working together is exactly what I’d love to see.
Right now, I use Spaces to keep Bookends open in one space, and DT in another-- so, if I need to get a reference I hot-key switch spaces, find the citation, Shift-Cmd-Y to select and go back to DT, then Cmd-V to insert. It would be a lot nicer if I could do all of that with 1 or two mouse clicks.
I do much the same thing in Scrivener, while I’m writing.