There seems to be a certain perception that calibre isn't "real" software because it doesn't come in a shrink-wrapped box and take a multi-hundred-dollar hit out of your credit card. Therefore, people seem to think that the developer should be not only willing but eager to throw out the entire design philosophy in order to comply with their personal preference -- which is, generally, to store metadata in the filesystem. I'm curious, by the way: have you gone to the Mendeley developers and demanded that they rewrite their software to play nice with calibre? And if not, why not?
Calibre is not meant to be a cross-linking and citation system for research papers. It's a program for managing and organizing your ebooks and reading devices, for converting between formats, for collecting news for offline reading ... it's a lot of things. But no one program can do everything, and the fact that Mendeley exists -- an entire package devoted to managing research papers -- is something of a hint that it's a very large and complex task on its own, and not something likely to be added into (or even, really, considered during the design of) a general purpose ebook manager.
Like most of the people who start these threads, you're starting out with misconceptions about how calibre works, about how it is supposed to work, and about the tools provided. For example, you wrote:
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1) It makes it easier to share batches of files with others. If I want to transfer all of my fiction, but nothing else, to someone's memory stick/computer/whatever then all I have to do is move the Fiction folder. I don't have to hunt through my Calibre Library folder trying to sort out which Author folder is fiction and which isn't, to say nothing of the problem of an author who writes both fiction and nonfiction.
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That's using the filesystem as metadata. What we calibre users do, in that case, isn't search through any directory structure at all. If I want to give someone all my fiction, I tell calibre to export all the books tagged "fiction" onto the memory stick. No searching, no folders, no authors ... just click the "fiction" tag, control-A to select all the books it brings up, then export.
And if I want, I can tell it to export all my alternate-history science fiction that isn't military-themed, or all David Weber's science fiction but not his fantasy, or all the books that Eric Flint wrote unless they were co-written with David Drake ... you're starting to get the picture.
You're never supposed to hunt through your calibre library folder for anything, actually. The user interface is so much more powerful a tool for finding any given book than any file browser could possibly be. We had a fellow a while back who ranted about how bad calibre was because he wanted to be able to store his books by subject: science -> chemistry -> inorganic chemistry -> intermetallic phases, I believe the example was. Which might have been fine as far as it went, but what if he owned a book that covered several different subjects in inorganic chemistry? Where would he store that? How could he find it? In calibre, he'd simply give the book a tag for each subject it covered -- "intermetallic phases" and "making things go boom" for example -- and be able to search for it under either tag.
We worry about wasted storage space, or most of us do, because we remember the days when, say, a 1.2gb drive cost me $365 at a computer show, and I was delighted to have haggled for such a good deal. Nowadays, drives are under $100 a terabyte. We really do not have to worry about saving storage space anymore. At least, not the amount that ebooks take up -- even if we duplicate our libraries for benefit of stubborn research paper organizing programs that insist on using the filesystem for metadata.
Just out of curiosity, take a look at how much space your whole library is taking up. Would it all fit on one DVD? Based on the price of a 1tb external drive in the buy.com sale flyer that arrived as I was typing this, that's 45 cents worth of HD space. I'm pretty sure a complete redesign of calibre would be more than 45 cents worth of work.
So manage your research papers in Mendeley. When you add new ones, just import those into calibre.
Y'know, all those books ought to be shoved into one huge indexed file, just to put an end to these threads.