I don't use Endnote, but I frequently edit Word documents whose bibliographies have been prepared using it. The following contains much extrapolation from personal impressions.
They have different ideas about use. Endnote is a bit more like Zotero than traditional Bibtex, stressing its access to official abstract and bibliography servers, with many users who have never either edited a bibliography entry themselves, or felt that they are maintainers of a bibliographic database, because they haven't felt the need. The idea is that that the professionals have taken care of the massive Endnote bibliographic database, so that you don't have to worry about it. This idea of being taken care of is supported by the work that the Endnote producers (recently Endnote was acquired by Thomson-Reuters, now one of the world's two giant news & professional information agencies) have put into cultivating a dialog with the major style guides, such as APA, so that their output is accepted by the authority as being in conformance with the official style.
The results are pretty good, but not as good as users expect. Very commonly I received manuscripts from clients who say I don't need to look at the bibliography because it was prepared with Endnote. I then look over the bibliography to see if I find any errors. Inevitably I do, occasionally serious ones, which I report back to the sometimes very surprised client.
Endnote allows export to Bibtex format. If you do so, the promises about conformance to style guides become worthless, as the Endnote representation of reference metadata does not cleanly correspond to Bibtex's. I have the idea that the same problems will apply if one tries to convert Endnote's format into the new Word 2010 reference format, but I have not confirmed this.
Bibtex is free. The standard Endnote package has an RRP of $300, and will require fairly frequent paid upgrades for most of its users.
To parse BibTeX format files, Biber uses a C library called "btparse" which is, for all intents and purposes, 99.9% compatible with BibTeX. So, You should rarely have problem using Biber as a drop-in replacement for BibTeX. As mentioned by others, the issue is rather the slightly different data model which biblatex has compared with the data model in BibTeX.
So, your question really relates to the difference in data models between plain BibTeX and BibLaTeX, regardless of whether you are using Biber as the biblatex backend. Be aware that in the future, around BibLaTeX 2.x, BibTeX will no longer be supported as a biblatex backend as it has too many limitations. Of course BibTeX format data files will always be supported.
The more important question is, as you mention, what the advantages of Biber might be even if you are not using any of the biblatex data model specifics. Here are some advantages of Biber in this respect (you can get an idea by searching for the string "Biber only" in the biblatex manual), omitting the features which require data source changes:
- Support of data sources other than
.bib (currently RIS, Zotero RDF/XML, Endnote XML)
- Support for remote data sources (
.bib files available via ftp or http)
- Support of other output formats (in 0.9.8 it will support GraphViz .dot output for
data visualisation and conversion to the planned biblateXML format)
- Full Unicode 6.0 support (including file names and citation keys)
- A sorting mechanism which I think is probably as good or better than any commercial
product - full Unicode, multi-field, per-field case and direction, CLDR aware and
completely user configurable. BibTeX doesn't come close in this regard.
- Automatic name and name list disambiguation. I think this is quite an impressive feature.
See section 4.11.4 of the
biblatex manual for a very good explanation of this with examples.
- Completely customisable crossref inheritance rules. BibTeX has a very basic static rule
only.
- Automatic encoding and decoding, including UTF-8 <-> LaTeX macros
- Very flexible configuration file "sourcemap" option which can be used to change the
.bib data as it is read by Biber, without changing the actual data source itself. You
can use this to do all sorts of things like drop certain fields, add fields,
conditionally drop/add fields, change fields using full Perl 5.14 regular expressions
(see Biber manual section 3.1.2).
This last feature is particularly interesting for you as you can potentially map your pure BibTeX .bib files into the biblatex model on the fly as Biber reads them but without altering the files. It's also very useful for dropping fields like abstract which often cause trouble due to LaTeX reserved characters.
There are also some other features implemented in Biber which are available in BibLaTeX 2.x:
- Customisable labels
- Multiple bibliographies in the same refsection with their own sorting/filtering
- "Related" entries - a general solution to the issue of all these "reprinted as",
"translated as" etc. requirements.
I forgot to mention that Biber automatically applies the BibLaTeX field and entrytype mappings (address -> location etc.) mentioned in the documentation. It does this by implementing some driver-level source mappings (see \DeclareSourcemap and its variants in the biblatex documentation).
Best Answer
You should not mix up the the bib file-format and bibtex. Bibtex is a program that sorts and formats entries of the bib-file according to a style you specify. Bibtex has a few disadvantages, especially now when more and more people use utf8 as a file encoding.
The problem of using a bib file with bibtex was always that you had to chose a style (
\bibliographystyle) which is rather difficult to customise.Biblatex is now a novel way of managing the look of your ciations in the text and the entries in the bibliography. As a backend (for sorting and such things) it can use either bibtex or biber. Biber is certeinly the future as it supports utf8, improved crossref's and more.
Biblatex still uses a bib file as database, so this is not outdated.
Now when you start from scratch, it is advisible to use biblatex because it is so easy to customise as it uses latex-macros. Your database can still be a bib file and you can use a tool such as jabref, mendeley, zotero or ... to maintain it